[1] "ofn"        "-oTBRCA-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/BRCA-TP/15076769/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/15086289/transformed.cor.cli.txt"

nPatients in clinical file=1080, in cluster file=1080, common to both=1062
[1]   82 1062
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              201               861 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              201               861 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              694               368 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              694               368 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               940 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               940 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73               989 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73               989 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              134               928 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              134               928 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              211               851 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              211               851 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75               987 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75               987 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               72               990 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               72               990 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              311               751 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              311               751 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              209               853 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              209               853 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              205               857 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              205               857 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              147               915 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              147               915 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              307               755 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              307               755 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              262               800 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              262               800 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              285               777 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              285               777 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              520               542 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              520               542 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              141               921 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              141               921 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              118               944 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              118               944 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               212                850 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               212                850 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               123                939 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               123                939 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               135                927 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               135                927 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                92                970 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                92                970 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               226                836 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               226                836 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               190                872 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               190                872 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                90                972 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                90                972 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               141                921 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               141                921 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                86                976 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                86                976 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               458                604 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               458                604 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               140                922 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               140                922 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               104                958 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               104                958 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               213                849 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               213                849 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               174                888 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               174                888 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               149                913 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               149                913 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               188                874 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               188                874 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               220                842 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               220                842 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               411                651 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               411                651 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               445                617 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               445                617 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               195                867 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               195                867 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                98                964 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                98                964 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              150               912 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              150               912 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              135               927 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              135               927 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              239               823 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              239               823 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               51              1011 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               51              1011 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              179               883 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              179               883 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              209               853 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              209               853 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              183               879 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              183               879 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              100               962 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              100               962 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              347               715 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              347               715 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              307               755 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              307               755 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              138               924 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              138               924 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              222               840 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              222               840 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              184               878 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              184               878 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              271               791 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              271               791 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              109               953 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              109               953 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              118               944 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              118               944 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              393               669 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              393               669 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               91               971 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               91               971 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              306               756 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              306               756 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              278               784 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              278               784 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               168                894 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               168                894 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               225                837 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               225                837 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               269                793 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               269                793 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               360                702 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               360                702 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               146                916 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               146                916 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               126                936 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               126                936 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               427                635 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               427                635 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               261                801 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               261                801 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               314                748 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               314                748 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               171                891 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               171                891 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               580                482 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               580                482 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               569                493 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               569                493 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               270                792 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               270                792 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               314                748 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               314                748 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               316                746 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               316                746 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               187                875 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               187                875 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               157                905 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               157                905 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                92                970 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                92                970 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                54               1008 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                54               1008 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               178                884 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               178                884 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               470                592 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               470                592 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              186               876 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              186               876 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              187               875 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              187               875 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 1062 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=127,	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=719,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            315     412    
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=44,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 1062 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "NUMBER_OF_LYMPH_NODES"                 
[10] "RACE"                                  
[11] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=65, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
272 616 130  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
272 616 130  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
272 616 130  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
272 616 130  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
501 350 117  75 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
501 350 117  75 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
501 350 117  75 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
501 350 117  75 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=31, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED   180  19
  1P GAIN WILD-TYPE 736 109
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              199               845 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               19               109 
$`1P GAIN MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SF TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
       42.81        48.10         7.96        19.20        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX 
      101.98        36.13        24.79        75.25         5.19        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EO TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 
       67.33        33.76        80.28        44.88        17.13         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YM TCGA-A2-A1G0 
       20.75        49.48        18.61        19.33        31.73        20.25 
TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0DA 
       42.44        33.93        50.37        38.37         7.30        35.67 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I 
       31.73        25.15        29.56        31.36        24.26        21.73 
TCGA-A7-A3IZ TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       10.59        14.50        21.17        11.05        10.29         9.37 
TCGA-A8-A06Z TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09M 
        1.02         9.99        24.99         0.99        43.00        33.07 
TCGA-A8-A09R TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3W6 TCGA-AC-A5XS 
        8.98        99.35        36.99         2.27        19.79         1.55 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A04C 
       13.71        18.67        13.58         0.03         1.12         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL 
        1.71         9.96         7.36         0.16         0.33         7.59 
TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0JB TCGA-AO-A0JD 
        7.04         0.33        68.75        32.78        50.70        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F 
       21.37        26.24       106.78       108.03        64.04        48.36 
TCGA-AQ-A04L TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI TCGA-AR-A1AK 
      130.09        32.91        74.79        86.66        61.84        51.25 
TCGA-AR-A24K TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-B6-A0I2 
       50.89        83.77        73.18        40.54        20.38       143.38 
TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RU TCGA-B6-A0X1 TCGA-B6-A1KC 
      149.59        65.72       112.37       131.21       186.48        43.59 
TCGA-B6-A408 TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BF TCGA-BH-A0BL 
       68.12        20.45        39.55        56.98        25.71        44.05 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DS 
       49.05        48.13        42.90        13.91        48.23         2.56 
TCGA-BH-A0DV TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A1F0 
       67.86         9.63        31.00        41.00        20.38        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A5IZ 
       31.53        97.48        72.07        72.07        38.60        18.64 
TCGA-C8-A12M TCGA-C8-A12V TCGA-C8-A135 TCGA-C8-A1HM TCGA-C8-A278 TCGA-C8-A27B 
       11.77        12.66         1.05         2.30         9.50         0.99 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.02        20.88        14.17        14.17        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XC 
       15.78        20.09        13.32        18.58        27.58        12.39 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A27R TCGA-E2-A109 
       21.83        14.50        12.66        16.54        10.09        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z 
       40.41        40.11        47.15        38.60        31.96        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15K TCGA-E2-A1AZ 
       25.41        27.12        19.43        25.05         9.04        60.53 
TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E9-A1N6 
       33.70        27.42        39.62       106.75       102.61        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A226 
       12.00        35.77        35.24        32.09        34.59        34.13 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P0 
       30.18        15.72        16.57        25.94        22.82        41.13 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DD 
        7.86        19.99        10.16       109.87        59.57        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A441 
       70.85        72.10        62.43        13.22         7.10        11.44 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D7 TCGA-OL-A5RW 
       14.47        14.79        16.08        15.68        58.52        36.36 
TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       20.38        28.21         8.91         9.93        13.12        16.93 
TCGA-Z7-A8R6 
      107.05 

$`1P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68        31.79        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X 
      104.81        18.02        78.41       121.94        63.12        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       75.55        98.99       107.93        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        50.43        44.28        17.52 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YL TCGA-A2-A0YT 
       18.21        50.47        21.90        21.67        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        17.36        60.72        22.45        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       49.48        47.31        34.98        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       35.47        30.61        37.45        33.11        29.79        20.19 
TCGA-A7-A13G TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX 
       13.74        17.92        14.73        12.10        10.72        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       29.03        31.00        26.01        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
       32.05        10.98         8.98         7.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00        31.00        33.01       112.08        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM 
        1.48        38.53        40.57        55.43        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70        33.04         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V 
       22.19        14.99        16.57        23.24        24.79        11.44 
TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR 
       17.42        12.26         1.68         8.22        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        2.96         6.51         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.96         7.00         7.17         6.28         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        95.70        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE 
       20.32        22.36        53.03        21.53        50.86        76.77 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      108.72        90.58        98.27        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93         5.65        15.62        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
       19.20       111.32        73.64         5.26        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        75.55        52.77        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       87.22        97.84        76.01        53.36        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       79.00        89.00        78.48        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      143.21        20.25        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG 
       77.62        12.13       220.90       129.57        50.70       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       129.57       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       58.88       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
       74.99       103.63        71.15        24.53        59.84        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.16        48.36        56.94 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        24.85        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD 
       45.57        49.94        11.67        41.75        44.02        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DP 
       31.17        23.44        38.01        22.13        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        3.22        38.47        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
       14.30        44.81        46.19        32.58        24.49        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       23.08        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 
       42.28        12.00        55.69        49.58        17.69        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        45.63       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28         8.94        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       12.20         0.03         0.23        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 
       11.90        13.25        20.58        13.97        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       19.20        17.49        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.12        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        14.70        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       23.90        18.15        17.16        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        15.55        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        15.16        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
        9.44        16.41        13.48         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10B 
        8.02        12.10        43.00        34.42        27.52        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       28.44        28.87        44.68        40.96        38.24        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A153 
       33.30        43.33        34.26        32.02        28.60        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        26.56        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        36.82        13.12        36.56        39.55        12.59 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        6.12         3.02         2.76        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
        1.12        34.65         6.58        21.27        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       12.53        13.32        39.09        22.75        41.03        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       23.51        20.71        17.06         0.69        27.22         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56         0.72        29.72         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41        12.33        23.84        14.70         0.79        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2DA TCGA-GM-A2DB 
       34.03        17.49        23.51         7.40       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       83.34        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12         2.60        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24        13.28        10.62        24.95        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       17.06        15.32        14.70        22.26         2.63         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73        40.11        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        0.26        16.50        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        29.03        15.35        16.04       108.07 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           186.48            234.28 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            25.94             23.84 
[1] "0.0 - 186.5 (25.9)" "0.0 - 234.3 (23.8)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED        16       14        1        0        70        52
  1P GAIN WILD-TYPE      73       67        7        3       283       193
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           0         23          6         12        3
  1P GAIN WILD-TYPE         2        127         23         51       17
                   vv
clus                STAGE TIS STAGE X
  1P GAIN MUTATED           1       0
  1P GAIN WILD-TYPE         0      13
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 16                73
  STAGE IA                14                67
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               70               283
  STAGE IIB               52               193
  STAGE III                0                 2
  STAGE IIIA              23               127
  STAGE IIIB               6                23
  STAGE IIIC              12                51
  STAGE IV                 3                17
  STAGE TIS                1                 0
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    38 130  23   9
  1P GAIN WILD-TYPE 234 486 107  31
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              38               234
  T2             130               486
  T3              23               107
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED   104  64  19  13
  1P GAIN WILD-TYPE 397 286  98  62
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0             104               397
  N1              64               286
  N2              19                98
  N3              13                62
[1] 4 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   165   3
  1P GAIN WILD-TYPE 714  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    165    3
  1P GAIN WILD-TYPE  714   18
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0             165               714
  1               3                18
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   199   2
  1P GAIN WILD-TYPE 852   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    199    2
  1P GAIN WILD-TYPE  852    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE             199               852
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P GAIN MUTATED                            0                           157
  1P GAIN WILD-TYPE                          1                           606
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P GAIN MUTATED                               20                   3
  1P GAIN WILD-TYPE                            172                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P GAIN MUTATED                       2                                7
  1P GAIN WILD-TYPE                     2                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1P GAIN MUTATED                    1             11
  1P GAIN WILD-TYPE                 16             37
D1V8, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                157               606
  INFILTRATING LOBULAR CARCINOMA                20               172
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                11                37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    67 134
  1P GAIN WILD-TYPE 221 640
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     67  134
  1P GAIN WILD-TYPE  221  640
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               67               221
  YES             134               640
[1] 2 2
[1] FALSE
D1V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     7
  1P GAIN WILD-TYPE                                0    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          42   140
  1P GAIN WILD-TYPE                       128   596
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     42               128
  WHITE                                        140               596
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5 168
  1P GAIN WILD-TYPE  33 690
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5  168
  1P GAIN WILD-TYPE   33  690
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                33
  NOT HISPANIC OR LATINO             168               690
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   608  76
  1Q GAIN WILD-TYPE 308  52
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              684               360 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               76                52 
$`1Q GAIN MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        42.81        40.14        48.56        48.36         9.96 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN 
       43.43        48.10        47.24        20.88         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       19.20        18.21        78.41        73.84        87.25       101.98 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CS 
       36.13       136.73        24.79       114.81        88.60        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       75.25         5.19        98.99        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ 
       61.58        25.22       101.72       134.40        80.28        79.76 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        31.82        63.29        99.19        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A25A 
       31.73        23.77        23.47        22.45        20.25       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       42.44        17.19       105.34        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S2 
       83.01        29.98        50.37        38.37         7.30        21.14 
TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       38.30        35.47        30.61        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        21.73        20.61        10.59        10.29        11.28 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
        9.37        10.42        13.02         1.02        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       18.97         9.99         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        15.06         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       19.96        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        49.05        45.07        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       25.02         8.98        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C 
       19.04        13.02        21.04        27.02        17.03         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         5.72         1.48        38.53        99.35 
TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       40.57        36.99        26.04        50.70         0.92         2.27 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YJ 
       16.31        14.83        14.99        16.57        19.79        24.79 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.68        20.19         1.12         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         1.78         1.71         9.96         7.36 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.16         0.33         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XW 
        0.33         0.33        12.33         0.30         0.33         5.59 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       81.63        68.75        32.78        26.04        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       53.03        21.53        50.70        72.00        21.37        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 
       62.04        55.33        71.80        99.25       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ 
       90.58        98.27        64.04        48.36        41.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 
       70.39        17.79        24.79       130.09         5.65        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.91        19.20       111.32         5.26        74.79        86.66 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY 
       43.73        39.98        37.81        61.28        63.62        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q 
       50.89        94.22        96.89        78.51         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       87.22        50.96        83.77        89.00        73.18        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       93.83       143.21        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO 
      129.57        65.72       112.37       176.98        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RN 
      110.93       140.88       211.56       189.01       234.28       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WT TCGA-B6-A0WV 
      162.05       102.77       100.70       131.21       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X7 
       18.35        21.47       129.57       129.70       186.48        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52        73.51       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       68.12       103.63        71.15        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       28.50        46.95        40.83        39.55        48.36        56.98 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       44.05        61.68        35.67        27.19        53.95        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 TCGA-BH-A0E6 
        2.56        38.47        67.86        47.41        15.68         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H3 
       46.19        32.58        24.49        31.00        15.16        37.78 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       23.08        41.00        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A18F 
       36.85        12.89        27.25         5.59        23.93         8.81 
TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
        2.01        90.84        26.66        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        12.00        55.69        49.58        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU 
       97.48        63.35        55.00        45.63        72.07        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        26.14        38.60       130.16         6.44        20.12 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 
       18.64        23.51         9.63         5.26         9.70        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12V 
        9.44        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE 
       12.66         0.39         3.16         2.24         1.05        12.33 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X 
       11.28        12.03        10.42         2.30         3.25         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 
        0.03         0.23        13.02        13.41        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        14.17        21.14        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        18.58        16.73        25.74 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15        12.39        15.22        14.73        21.83 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        15.55        15.85        16.31         6.35        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G 
       12.66        16.54        15.52         9.93        14.14        13.45 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       14.43         9.44         4.80        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 
       12.26        33.37        16.18         8.02        12.10        34.42 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V 
       47.15        44.68        38.24        38.60        33.30        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        28.60        18.51        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       19.43        25.05        23.34        17.29        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15T 
       12.92        19.40         9.04        20.58        11.05        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG 
       60.53        53.62        32.35        17.10        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 
       33.73        33.70        28.44         3.88        22.19        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       27.42        39.62        19.66        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A574 
        8.75        16.93         5.52        15.72         8.28        26.56 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
       12.85        13.48        12.00        13.12        36.56        35.77 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       35.24         9.86        11.90        34.95         2.56         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        32.09        32.09         1.12         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G 
       34.59        34.13        32.05        39.09        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.71        17.06         0.69         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       29.72        26.07        30.18        15.72        23.84        14.70 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       14.40        15.39        12.20        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P3 
       25.94        22.82        29.95        29.85        41.13        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH 
       23.11         7.86        19.99         6.15        10.52        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       55.00        52.73        25.91        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      109.87        59.57        83.34        75.02        70.85        72.10 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
      101.62       110.50        38.20        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        11.44        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        7.46        14.70        14.07        27.91        22.39         2.10 
TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ 
       20.38        41.92        26.04        17.36        28.21        19.73 
TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
        8.91        64.21        86.96         9.93        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       16.93        16.80        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        52.96        29.03        15.35       108.07       107.05 

$`1Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14        11.44         8.52        14.37        14.27        13.68 
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04V 
       31.79        28.01       104.81        18.02       121.94        63.12 
TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 
       55.43        99.12        92.48       107.93       107.93        34.55 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX 
      107.61        74.40        72.00        34.29        61.94        24.72 
TCGA-A2-A0SU TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 
       54.64        18.21        50.47        17.36        60.72        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3XV 
       19.56        16.47        52.47        18.15        10.59        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       49.48        47.31        34.98        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A0DC 
       26.96        21.90        35.31        34.29        37.45        29.79 
TCGA-A7-A13G TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3RF TCGA-A7-A6VY TCGA-A8-A06P 
       23.61        22.32        11.34        13.41         8.75        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A07I TCGA-A8-A07J 
       17.98        53.06        29.03         9.01        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08I 
       32.05        10.98        18.05        36.95        13.02        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09D 
       37.05         9.99        31.00        33.01        33.01        50.04 
TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A2FF TCGA-AC-A2FK 
        1.02        19.04         0.99        38.04        55.43        38.79 
TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A62V TCGA-AC-A7VB 
       33.04        32.45        22.19        23.24        11.44         8.22 
TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
        0.03         1.32         2.30         2.96         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         6.44         5.65         7.96         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        0.33         5.33        80.28        61.35        66.77        95.70 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        52.18        37.48 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12E 
       50.86        76.77        50.24       102.58       108.72        57.30 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A1H2 
       28.37        14.73        82.62         0.53        26.93        15.62 
TCGA-AQ-A54N TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        2.56        73.64        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       101.95        83.87       114.02        85.97 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24H 
       43.56        43.07        17.23        76.21        62.14       160.90 
TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z 
       84.20        97.84        76.01        53.36        85.35        79.00 
TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0IC TCGA-B6-A0IG 
       78.48        58.92        20.25        10.59        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RQ 
       18.77       126.12        68.45        81.17        78.02       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 
       89.46       157.41        97.48       113.79        28.27        68.94 
TCGA-B6-A1KN TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BP 
      139.17        59.84        39.16        56.94        51.68        48.69 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ 
       53.69        49.94        11.67        31.17        38.01         3.22 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0GY 
       16.27         4.41        14.30        44.81        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW 
       10.78        35.51        24.56        52.96        26.50        51.32 
TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I 
       50.79        24.95        42.35        44.81        23.05         7.23 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY 
       20.12        72.56        37.74       113.82        82.85        17.69 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O 
      122.89        36.92       144.59        83.31        57.83        10.65 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ TCGA-C8-A12N TCGA-C8-A12Q 
       10.52       109.28         8.94        18.87        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
       12.66        12.66         1.87         1.12         4.11         4.08 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       10.92        11.34         0.16         0.30         0.23         0.43 
TCGA-C8-A27A TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A145 TCGA-D8-A147 
       12.20        12.49        19.46        11.90        13.48        19.20 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XD 
       12.03        14.01        21.01        17.79        23.90        17.16 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A1Y2 
       14.50        19.92        16.41        12.99        15.32        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P 
       17.42        16.04        13.05        16.41        13.48         0.76 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A14P TCGA-E2-A14S 
       18.51        21.67        43.00        27.52        40.96        33.17 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C 
       43.33        32.02        21.04        23.87        14.79        22.82 
TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       21.63        17.42        13.02        19.56        17.06        14.07 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IK 
       53.03        33.01        28.50        16.47        38.30        22.65 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL 
       20.98        11.08        24.59        40.47        28.90        43.04 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        34.29        34.82        32.88        36.82 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R6 
       39.55        12.59        25.84        28.27         6.12         2.76 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B 
       40.24        34.65        35.64        12.53        13.32        22.75 
TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54X 
       41.03        27.22         1.94         0.76        18.41        12.33 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.79        13.81        39.72         8.48        18.21        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       28.77        40.41        39.78        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 
       18.90        13.94        14.43        34.55        22.09        34.03 
TCGA-EW-A3U0 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       17.49       216.76        79.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-HN-A2NL 
      106.06        85.35        43.73        69.30        66.38         2.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
       10.62        24.95        10.95        14.50        12.36        14.73 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.30        31.99        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PL-A8LX 
       65.62        42.77        14.07        40.11        47.01         0.16 
TCGA-PL-A8LY TCGA-S3-AA10 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A89A 
        0.26        15.39        15.35        14.96        13.84        16.04 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           234.28            216.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           23.455            27.090 
[1] "0.0 - 234.3 (23.5)" "0.0 - 216.8 (27.1)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED        48       43        4        3       244       163
  1Q GAIN WILD-TYPE      41       38        4        0       109        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         93         23         46       13
  1Q GAIN WILD-TYPE         1         57          6         17        7
                   vv
clus                STAGE TIS STAGE X
  1Q GAIN MUTATED           1       8
  1Q GAIN WILD-TYPE         0       5
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 48                41
  STAGE IA                43                38
  STAGE IB                 4                 4
  STAGE II                 3                 0
  STAGE IIA              244               109
  STAGE IIB              163                82
  STAGE III                1                 1
  STAGE IIIA              93                57
  STAGE IIIB              23                 6
  STAGE IIIC              46                17
  STAGE IV                13                 7
  STAGE TIS                1                 0
  STAGE X                  8                 5
[1] 13  2
[1] TRUE
[1] "dimension of 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   151 428  83  30
  1Q GAIN WILD-TYPE 121 188  47  10
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             151               121
  T2             428               188
  T3              83                47
  T4              30                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   325 232  71  54
  1Q GAIN WILD-TYPE 176 118  46  21
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             325               176
  N1             232               118
  N2              71                46
  N3              54                21
[1] 4 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   570  13
  1Q GAIN WILD-TYPE 309   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    570   13
  1Q GAIN WILD-TYPE  309    8
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             570               309
  1              13                 8
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   688   6
  1Q GAIN WILD-TYPE 363   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    688    6
  1Q GAIN WILD-TYPE  363    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             688               363
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q GAIN MUTATED                            1                           482
  1Q GAIN WILD-TYPE                          0                           281
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q GAIN MUTATED                              150                   4
  1Q GAIN WILD-TYPE                             42                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q GAIN MUTATED                       2                               17
  1Q GAIN WILD-TYPE                     2                               13
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1Q GAIN MUTATED                    8             30
  1Q GAIN WILD-TYPE                  9             18
D2V8, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                482               281
  INFILTRATING LOBULAR CARCINOMA               150                42
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)              17                13
  MUCINOUS CARCINOMA                             8                 9
  OTHER  SPECIFY                                30                18
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   188 506
  1Q GAIN WILD-TYPE 100 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    188  506
  1Q GAIN WILD-TYPE  100  268
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              188               100
  YES             506               268
[1] 2 2
[1] FALSE
D2V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    33
  1Q GAIN WILD-TYPE                                0    27
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                         106   492
  1Q GAIN WILD-TYPE                        64   244
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         33                27
  BLACK OR AFRICAN AMERICAN                    106                64
  WHITE                                        492               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    20 560
  1Q GAIN WILD-TYPE  18 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     20  560
  1Q GAIN WILD-TYPE   18  298
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  20                18
  NOT HISPANIC OR LATINO             560               298
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   101  18
  2P GAIN WILD-TYPE 815 110
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              119               925 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18               110 
$`2P GAIN MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SO TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0SX 
      131.67        42.81        28.01        56.81        67.33        50.43 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XS 
       17.13         8.38        18.21        18.61        19.20        33.93 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       50.37        26.96        30.61        35.67        31.73        20.19 
TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
       21.73        21.17        12.10         1.02        17.98        31.00 
TCGA-A8-A075 TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y 
       17.03        24.99         0.99        12.00         5.72        17.42 
TCGA-AC-A6IW TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FX TCGA-AO-A0J2 TCGA-AO-A0JD 
       13.58         1.78         0.16         0.33        32.78        72.00 
TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A0TX 
      102.58        64.04        48.36        70.39        74.79        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A24Q TCGA-B6-A0I2 TCGA-B6-A0RE TCGA-B6-A0RU 
       65.36        83.87       104.28       143.38       211.56       131.21 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-BH-A0AW TCGA-BH-A0BG TCGA-BH-A0C0 
      129.57       186.48        74.99        20.45        24.85        41.75 
TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A18T TCGA-BH-A18V 
       44.02        48.23         9.63        46.19         7.36        51.16 
TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM 
       69.93        12.00        31.53        97.48       114.15        45.63 
TCGA-BH-A203 TCGA-BH-A5IZ TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A131 
       38.60        18.64        11.77        12.66        12.66         2.24 
TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A8HP TCGA-D8-A13Z 
       12.03         0.43         9.53         9.50        13.02        20.88 
TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JK TCGA-D8-A1XF TCGA-D8-A1XL 
       14.17        19.20        14.17        20.12        15.22        19.92 
TCGA-D8-A1XU TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P 
       12.99        13.48        10.09        46.59        40.11        40.96 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LK 
       14.79        25.05        23.34        33.70        28.90         8.75 
TCGA-E2-A574 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1IY 
       26.56         6.58        34.59        29.72         0.79         8.48 
TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
        6.15        55.00       109.87        79.10        75.02        70.85 
TCGA-HN-A2NL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A5RW TCGA-OL-A66I 
        2.60        14.70        14.79        14.70        36.36        23.47 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA10 TCGA-UL-AAZ6 
       14.07        28.21         9.93        15.39        17.03 

$`2P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 
       75.55        75.25         5.19        98.99       107.93        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        61.58        25.22       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.88        44.28        17.52        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15       105.34        10.59        20.88        39.65        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        49.48        47.31        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        17.92        14.73        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W 
       32.05         9.99        10.98         8.98         7.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       38.01        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       11.44        13.71        18.67        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         6.51         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        21.40        52.18        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY 
       73.64         5.26        86.66        42.35        98.93        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      107.24       101.95       114.02        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        33.73       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       96.89        78.51        84.20         2.76        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       89.00        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      143.21        20.25        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        10.59        77.62       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      162.05       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        24.53        59.84        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 
       53.95        45.57        49.94        11.67        49.05        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.39        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       49.58        17.69        25.81        89.16        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 
       72.07       144.59        72.07        28.14        26.14        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28         8.94        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.28         0.16        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        0.03        12.20         0.99         0.03         0.23        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        11.90        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        21.14        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       23.90        27.58        18.15        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       21.83        14.50        17.69        15.55        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31         6.35        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43         9.44        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C 
       27.12        23.24        19.43        21.04        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       17.06        14.07        14.99        60.53        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.73        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        40.47        18.87       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        34.29        12.85        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       13.48        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
       32.09        32.09        40.24         1.12        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       22.75        41.03        12.89        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        14.70        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        19.96        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        83.34        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       15.32        14.47        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        16.50        13.12        16.93        16.80 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S 
       13.84        15.35        14.96        13.84        13.94         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.16              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           211.56            234.28 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            23.47             24.56 
[1] "0.2 - 211.6 (23.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         6        8        0        0        46        33
  2P GAIN WILD-TYPE      83       73        8        3       307       212
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           0         13          3          7        2
  2P GAIN WILD-TYPE         2        137         26         56       18
                   vv
clus                STAGE TIS STAGE X
  2P GAIN MUTATED           0       1
  2P GAIN WILD-TYPE         1      12
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  6                83
  STAGE IA                 8                73
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               46               307
  STAGE IIB               33               212
  STAGE III                0                 2
  STAGE IIIA              13               137
  STAGE IIIB               3                26
  STAGE IIIC               7                56
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    25  79  12   5
  2P GAIN WILD-TYPE 247 537 118  35
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              25               247
  T2              79               537
  T3              12               118
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    57  40  15   8
  2P GAIN WILD-TYPE 444 310 102  67
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              57               444
  N1              40               310
  N2              15               102
  N3               8                67
[1] 4 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   104   2
  2P GAIN WILD-TYPE 775  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    104    2
  2P GAIN WILD-TYPE  775   19
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             104               775
  1               2                19
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   122   0
  2P GAIN WILD-TYPE 929  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    122    0
  2P GAIN WILD-TYPE  929   11
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE             122               929
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P GAIN MUTATED                            1                           108
  2P GAIN WILD-TYPE                          0                           655
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P GAIN MUTATED                                4                   2
  2P GAIN WILD-TYPE                            188                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P GAIN MUTATED                       2                                0
  2P GAIN WILD-TYPE                     2                               30
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2P GAIN MUTATED                    0              5
  2P GAIN WILD-TYPE                 17             43
D3V8, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                108               655
  INFILTRATING LOBULAR CARCINOMA                 4               188
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                30
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 5                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    36  86
  2P GAIN WILD-TYPE 252 688
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     36   86
  2P GAIN WILD-TYPE  252  688
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               36               252
  YES              86               688
[1] 2 2
[1] FALSE
D3V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1    10
  2P GAIN WILD-TYPE                                0    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          31    69
  2P GAIN WILD-TYPE                       139   667
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     31               139
  WHITE                                         69               667
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0 104
  2P GAIN WILD-TYPE  38 754
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0  104
  2P GAIN WILD-TYPE   38  754
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO             104               754
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    63   8
  2Q GAIN WILD-TYPE 853 120
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               973 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8               120 
$`2Q GAIN MUTATED`
TCGA-3C-AALI TCGA-A1-A0SO TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0SX TCGA-A2-A0YE 
      131.67        28.01       101.98        56.81        50.43        18.21 
TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA 
       18.61        19.20        50.37        26.96        30.61        35.67 
TCGA-A7-A13D TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A07U 
       31.73        21.73        21.17        17.98        31.00        24.99 
TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AN-A04C TCGA-AO-A124 TCGA-AO-A12D 
       12.00         5.72        17.42         1.78       102.58        64.04 
TCGA-AO-A12F TCGA-AR-A24Q TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-BH-A0AW 
       48.36       104.28       129.57       186.48        74.99        20.45 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E9 TCGA-BH-A18T 
       24.85        44.05        44.02        48.23        46.19         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1F2 TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A12U 
       51.16        69.93        31.53        38.60        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A8HP TCGA-D8-A147 
       12.66         2.24         0.43         9.53        13.02        19.20 
TCGA-D8-A1J8 TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P 
       14.17        12.99        13.48        46.59        40.11        40.96 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1LE TCGA-E2-A574 TCGA-E9-A5FL TCGA-EW-A1IY 
       25.05        23.34        28.90        26.56         0.79         8.48 
TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-LL-A5YN TCGA-LL-A5YP 
        6.15        55.00       109.87        79.10        14.70        14.79 
TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A66I TCGA-PL-A8LZ TCGA-S3-AA10 
       15.68        36.36        23.47         9.93        15.39 

$`2Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        87.25        63.12        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       75.55        75.25         5.19        98.99       107.93        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        50.47        21.90        21.67        49.48 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        48.46        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       49.48        47.31        34.98        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       34.29        35.47        37.45        33.11        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        38.01        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       12.00        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95         2.37        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70        33.04         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        13.71        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        98.27        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        63.62        62.14        33.73       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22        96.89        78.51        84.20         2.76        87.22 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        89.00        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 
       79.63        18.35        21.47       113.79       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        68.12       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        41.75        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       31.17        23.44        38.01        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        26.14        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         0.39         3.16         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
        0.30         0.23         0.36         8.28         9.67         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        9.50        12.20         0.99         0.03         0.23        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        21.14        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        15.16        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       27.42        39.62        19.66        24.59        40.47        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72         8.28        30.61        34.92        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       41.03        12.89        23.51        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         7.13        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        14.70        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        19.96        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP 
       10.95        25.05        17.06        15.32        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63        16.08         7.46        14.50        14.70        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.73        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       58.52        31.99        58.62        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       42.77        26.04        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26        16.50        13.12        16.93        16.80        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.43              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           186.48            234.28 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            25.05             24.43 
[1] "0.4 - 186.5 (25.1)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         5        4        0        0        28        23
  2Q GAIN WILD-TYPE      84       77        8        3       325       222
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           0          5          2          4        1
  2Q GAIN WILD-TYPE         2        145         27         59       19
                   vv
clus                STAGE TIS STAGE X
  2Q GAIN MUTATED           0       0
  2Q GAIN WILD-TYPE         1      13
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  5                84
  STAGE IA                 4                77
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               28               325
  STAGE IIB               23               222
  STAGE III                0                 2
  STAGE IIIA               5               145
  STAGE IIIB               2                27
  STAGE IIIC               4                59
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    14  50   7   2
  2Q GAIN WILD-TYPE 258 566 123  38
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               258
  T2              50               566
  T3               7               123
  T4               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    37  23   7   4
  2Q GAIN WILD-TYPE 464 327 110  71
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              37               464
  N1              23               327
  N2               7               110
  N3               4                71
[1] 4 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    64   1
  2Q GAIN WILD-TYPE 815  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     64    1
  2Q GAIN WILD-TYPE  815   20
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              64               815
  1               1                20
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    73   0
  2Q GAIN WILD-TYPE 978  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     73    0
  2Q GAIN WILD-TYPE  978   11
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              73               978
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q GAIN MUTATED                            0                            64
  2Q GAIN WILD-TYPE                          1                           699
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q GAIN MUTATED                                3                   0
  2Q GAIN WILD-TYPE                            189                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q GAIN MUTATED                       2                                0
  2Q GAIN WILD-TYPE                     2                               30
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2Q GAIN MUTATED                    0              4
  2Q GAIN WILD-TYPE                 17             44
D4V8, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 64               699
  INFILTRATING LOBULAR CARCINOMA                 3               189
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                30
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 4                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    21  52
  2Q GAIN WILD-TYPE 267 722
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   52
  2Q GAIN WILD-TYPE  267  722
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               21               267
  YES              52               722
[1] 2 2
[1] FALSE
D4V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     8
  2Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          17    42
  2Q GAIN WILD-TYPE                       153   694
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     17               153
  WHITE                                         42               694
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  63
  2Q GAIN WILD-TYPE  38 795
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   63
  2Q GAIN WILD-TYPE   38  795
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              63               795
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED   113  19
  3P GAIN WILD-TYPE 803 109
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              132               912 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               109 
$`3P GAIN MUTATED`
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T2 
       24.79        75.55        98.99        27.12        50.43         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD 
       20.75        31.73        17.36        33.93        24.39        38.30 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        33.11        25.15        14.70        14.50        21.17 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A08B TCGA-A8-A08C 
       10.29        13.02         1.02         9.01        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 
       33.01        12.00        37.05        31.00        33.01        17.95 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q 
       12.00         9.99        12.00        49.05        29.98        25.02 
TCGA-A8-A09R TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AN-A03Y TCGA-AN-A0AS 
        8.98         5.72        26.04         2.27         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03O TCGA-AO-A0J4 
        0.36         0.33         0.33        12.33        81.63        52.18 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32       106.78        64.04        24.79         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24V 
       74.79        61.84        52.77        37.81        50.89        85.35 
TCGA-AR-A2LL TCGA-B6-A0IA TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS 
       66.15       220.90       140.88       211.56       102.77       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AU 
      131.21        79.63        43.59        85.35        68.12        24.53 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0DS 
       56.94        44.05        53.69        45.57        41.75         2.56 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N 
       46.19        24.49        20.38        27.25        50.79        37.74 
TCGA-BH-A18U TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A5J0 TCGA-C8-A12M 
       51.39       114.15        26.14        38.60        23.51        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A1HI TCGA-C8-A27B TCGA-D8-A13Z 
       12.66        12.66        12.66        11.28         0.99        20.88 
TCGA-D8-A147 TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A27R 
       19.20        27.58        16.41        15.16        14.24        10.09 
TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14T 
       12.10        46.59        37.51        47.15        44.68        33.30 
TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1IH 
       18.51        19.43        20.71        18.21        60.53        33.73 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A54Y 
       18.87       102.61        32.09        40.24         6.58        23.84 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P8 TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A3XL 
       14.40        28.77         7.86        19.96        70.85        69.30 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5RW TCGA-OL-A6VO TCGA-S3-A6ZF 
       15.32        14.79        16.08        36.36        28.21        16.50 

$`3P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        75.25         5.19       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        44.88        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        83.01        29.98        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        50.37        38.37         7.30        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       30.61        37.45        29.79        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        11.97        14.93        13.74        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        17.98        53.06        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        8.98         7.99        24.99         9.99        45.07        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08L 
       15.06        36.95        13.02         0.99        19.96         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       30.97        41.98         9.99         1.02        50.04        45.07 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       33.07         1.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95         2.37        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70        33.04         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        26.04        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       99.25       108.72       108.03        90.58        98.27        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39         0.53        17.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52        19.20       111.32        73.64         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        17.23        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        83.77        79.00        89.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       54.21        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59        12.13       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       162.05       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      139.17       170.17        74.99       103.63        71.15        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        48.36        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        24.85        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       48.69        27.19        53.95        49.94        11.67        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE 
       15.68        14.30         9.63        44.81        32.58        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK 
       24.56        23.08        41.00        52.96        26.50         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V 
       30.28        55.63        37.55        66.05         7.36        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       69.93        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       72.07        28.14        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
        0.39         3.16         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50        12.20         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        11.90        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        15.55        15.85        16.31         6.35        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       12.66        16.54        15.32        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18         8.02 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U 
       28.87        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        31.96        28.60        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       23.24        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        21.63        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       40.47        28.90       106.75         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         8.28        30.61        34.92        26.56 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.24        25.84         9.86        11.90        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        34.65        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       12.89        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       26.07        18.41        30.18        15.72        12.33        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        13.81        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       52.96        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        75.02        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       43.73        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       17.06        14.70        14.47        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        7.46        14.50        14.70        12.36        14.73        14.07 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       26.04        17.36        14.07        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       13.12        16.93        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.33              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           220.90            234.28 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           27.185            23.755 
[1] "0.3 - 220.9 (27.2)" "0.0 - 234.3 (23.8)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED        11        9        0        1        54        20
  3P GAIN WILD-TYPE      78       72        8        2       299       225
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           0         18          7          6        4
  3P GAIN WILD-TYPE         2        132         22         57       16
                   vv
clus                STAGE TIS STAGE X
  3P GAIN MUTATED           0       2
  3P GAIN WILD-TYPE         1      11
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 11                78
  STAGE IA                 9                72
  STAGE IB                 0                 8
  STAGE II                 1                 2
  STAGE IIA               54               299
  STAGE IIB               20               225
  STAGE III                0                 2
  STAGE IIIA              18               132
  STAGE IIIB               7                22
  STAGE IIIC               6                57
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    32  83   9   9
  3P GAIN WILD-TYPE 240 533 121  31
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              32               240
  T2              83               533
  T3               9               121
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    67  36  18  10
  3P GAIN WILD-TYPE 434 314  99  65
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              67               434
  N1              36               314
  N2              18                99
  N3              10                65
[1] 4 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   124   4
  3P GAIN WILD-TYPE 755  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    124    4
  3P GAIN WILD-TYPE  755   17
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0             124               755
  1               4                17
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   133   1
  3P GAIN WILD-TYPE 918  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    133    1
  3P GAIN WILD-TYPE  918   10
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE             133               918
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P GAIN MUTATED                            0                           113
  3P GAIN WILD-TYPE                          1                           650
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P GAIN MUTATED                                7                   2
  3P GAIN WILD-TYPE                            185                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P GAIN MUTATED                       0                                4
  3P GAIN WILD-TYPE                     4                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3P GAIN MUTATED                    1              7
  3P GAIN WILD-TYPE                 16             41
D5V8, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                113               650
  INFILTRATING LOBULAR CARCINOMA                 7               185
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 7                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    40  94
  3P GAIN WILD-TYPE 248 680
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     40   94
  3P GAIN WILD-TYPE  248  680
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               40               248
  YES              94               680
[1] 2 2
[1] FALSE
D5V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     8
  3P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          24    82
  3P GAIN WILD-TYPE                       146   654
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     24               146
  WHITE                                         82               654
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5 101
  3P GAIN WILD-TYPE  33 757
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5  101
  3P GAIN WILD-TYPE   33  757
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                33
  NOT HISPANIC OR LATINO             101               757
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   181  26
  3Q GAIN WILD-TYPE 735 102
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              207               837 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               26               102 
$`3Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D0 
       20.88        87.25        24.79        75.55        98.99        67.33 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       63.29        27.12        50.43        17.13         8.38        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       20.75        21.90        31.73        17.36        22.45        19.20 
TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       33.93        24.39        38.30        30.61        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       31.73        25.15        23.80        14.50        21.17        14.73 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A07J 
       10.29        10.42        13.02         1.02         9.01        12.00 
TCGA-A8-A07L TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       32.05        24.99         9.99        38.01        28.96        33.01 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
       12.00        31.00        33.01        17.95         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H 
       49.05        29.98        33.07        25.02         8.98         5.72 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A041 
       26.04         2.27        13.71        13.58         0.33         0.23 
TCGA-AN-A049 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FW 
        0.62         9.96         0.16         0.33         7.59         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J4 
        0.33         0.33        12.33        80.28        81.63        52.18 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32       106.78        64.04        70.39         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24M 
       74.79        61.84        52.77        37.81        50.89        96.89 
TCGA-AR-A24V TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LL TCGA-AR-A5QP TCGA-B6-A0I2 
       85.35        58.92        93.83        66.15        20.45       143.38 
TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RP TCGA-B6-A0RS 
      220.90       176.98        18.77       140.88       102.77       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A401 TCGA-B6-A408 
      131.21        79.63        43.59       101.52        85.35        68.12 
TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 
       24.53        56.94        44.05        53.69        45.57        41.75 
TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0HI 
       48.23         2.56        46.19        24.49        23.08        20.38 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18U 
       12.89        27.25        50.79        37.74        55.63        51.39 
TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 
       51.16        12.00       114.15        72.07        26.14        38.60 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12M TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       18.64        23.51        11.77        12.66        12.66        12.66 
TCGA-C8-A1HI TCGA-C8-A26W TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-D8-A13Z 
       11.28         0.23         0.99         0.23        13.02        20.88 
TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XK 
       14.17        19.20        18.58        27.58        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A27R 
       19.92        16.41        12.99        15.16        14.24        10.09 
TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Z 
       12.10        46.59        37.51        47.15        44.68        18.51 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1IE 
       19.43        25.05        20.71        18.21        60.53        38.30 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       33.73        33.70        18.87       106.75       102.61        43.04 
TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF 
       34.92        12.00        35.24        32.09        40.24         6.58 
TCGA-E9-A1RH TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OW 
       34.59        23.84         0.79        14.40        28.77        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FS 
       29.82         7.86        19.99         6.15        19.96        52.73 
TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL 
        7.40        79.10        70.85        72.10        69.30         2.60 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5RW 
       15.32        14.79        16.08        15.68        14.73        36.36 
TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       20.38        28.21        86.96         9.93        16.50        16.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UU-A93S 
       16.80        15.39         3.81 

$`3Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       75.25         5.19       107.93        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       79.76        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       61.94        24.72        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.52        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G4 
       48.46        23.77        23.47        60.72        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
      105.34        10.59        20.88        39.65        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13E 
       35.31        34.29        35.47        37.45        29.79        20.19 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       23.61        29.56        31.36        24.26        23.74        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       12.10        10.72        11.05         9.37         8.75        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03        53.98        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07Z 
       14.01         9.99        10.98         8.98         7.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G 
       18.05        15.06        36.95        13.02         0.99        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       43.00        40.01        30.97        41.98        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V 
        1.02        50.04        45.07         1.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       36.99        38.79        50.70        33.04         0.92        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        17.42        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C 
        1.32         2.30         0.33         0.33         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         6.51         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.96         7.00         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        26.04        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       99.25       108.72       108.03        90.58        98.27        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52        19.20       111.32        73.64         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        17.23        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       33.73       160.90        94.22        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
      104.28        87.22        97.84        76.01        53.36        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        89.00        78.48        73.18        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      143.21        20.25        62.86        54.21        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QQ 
       39.39        40.54        20.38        54.74        16.04        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       149.59        12.13       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       112.37       126.12        84.59       110.14       110.93 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       162.05       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN 
      186.48        28.27        68.94        58.88        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
      170.17        74.99       103.63        71.15        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       48.36        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       27.19        53.95        49.94        11.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT 
       22.13        13.91        17.26        15.65         3.22        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       51.32         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       26.66        72.56        30.28        37.55        66.05         7.36 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       69.93        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07        28.14 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       10.52       109.28         8.94         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       11.77        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A8HQ 
        9.53         0.03         9.50        12.20         0.03        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        11.90        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       14.73        17.69        15.55        15.85        16.31         6.35 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       12.66        16.54        15.32        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18         8.02 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       28.87        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       43.33        34.26        32.02        31.96        28.60        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       27.12        23.24        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        21.63        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        17.10        37.41        32.78        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        16.93         5.52        15.72         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       26.56        34.29        12.85        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       13.48        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD 
        6.12         3.02         2.76        21.21        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       34.65        21.27        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       13.32        39.09        22.75        41.03        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       20.71        17.06         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       30.18        15.72        12.33        14.70        13.81        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
       18.90        13.94        10.52        14.43        34.55        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI 
      109.87        59.57       216.76        83.34        75.02        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       17.06        14.70        14.47        22.26         2.63         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        14.70        12.36        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       19.73        40.11         8.91        47.01        64.21         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26        13.12        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       13.94        17.03        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           220.90            234.28 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            24.53             24.56 
[1] "0.2 - 220.9 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED        15       15        1        1        82        41
  3Q GAIN WILD-TYPE      74       66        7        2       271       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           0         27         11         10        5
  3Q GAIN WILD-TYPE         2        123         18         53       15
                   vv
clus                STAGE TIS STAGE X
  3Q GAIN MUTATED           0       1
  3Q GAIN WILD-TYPE         1      12
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                15                66
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA               82               271
  STAGE IIB               41               204
  STAGE III                0                 2
  STAGE IIIA              27               123
  STAGE IIIB              11                18
  STAGE IIIC              10                53
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    45 133  20  13
  3Q GAIN WILD-TYPE 227 483 110  27
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              45               227
  T2             133               483
  T3              20               110
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED   109  60  24  14
  3Q GAIN WILD-TYPE 392 290  93  61
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             109               392
  N1              60               290
  N2              24                93
  N3              14                61
[1] 4 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   185   5
  3Q GAIN WILD-TYPE 694  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    185    5
  3Q GAIN WILD-TYPE  694   16
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             185               694
  1               5                16
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   210   1
  3Q GAIN WILD-TYPE 841  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    210    1
  3Q GAIN WILD-TYPE  841   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE             210               841
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q GAIN MUTATED                            0                           179
  3Q GAIN WILD-TYPE                          1                           584
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q GAIN MUTATED                                9                   4
  3Q GAIN WILD-TYPE                            183                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q GAIN MUTATED                       2                                6
  3Q GAIN WILD-TYPE                     2                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3Q GAIN MUTATED                    1             10
  3Q GAIN WILD-TYPE                 16             38
D6V8, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                179               584
  INFILTRATING LOBULAR CARCINOMA                 9               183
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                10                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    63 148
  3Q GAIN WILD-TYPE 225 626
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63  148
  3Q GAIN WILD-TYPE  225  626
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               63               225
  YES             148               626
[1] 2 2
[1] FALSE
D6V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1    13
  3Q GAIN WILD-TYPE                                0    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          46   127
  3Q GAIN WILD-TYPE                       124   609
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     46               124
  WHITE                                        127               609
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     6 168
  3Q GAIN WILD-TYPE  32 690
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6  168
  3Q GAIN WILD-TYPE   32  690
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                32
  NOT HISPANIC OR LATINO             168               690
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    64   9
  4P GAIN WILD-TYPE 852 119
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               73               971 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               119 
$`4P GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0ET TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        35.05        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06O TCGA-A8-A075 
       20.25        26.96        13.74        21.17        13.02        17.03 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T 
        9.01        18.97         9.99        19.96        33.01       112.08 
TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A0A9 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 
       33.01        29.98        27.02        33.04         2.27        16.57 
TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0JD TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW 
        1.78         0.33        72.00        32.91        74.79        98.93 
TCGA-AR-A2LL TCGA-B6-A0RG TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0DL 
       66.15        68.45        24.53        25.55        22.13        48.23 
TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EX 
       27.25        26.66        37.74        69.93        55.69        49.58 
TCGA-BH-A1FM TCGA-BH-A202 TCGA-C8-A1HN TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JG 
       45.63        26.14         3.25        14.17        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
       14.01        13.32        15.32        13.48        10.09        12.26 
TCGA-E2-A109 TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A1LA TCGA-E2-A56Z 
       46.59        33.17        27.12        20.71        24.59         8.28 
TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A22D TCGA-E9-A247 
       13.12         2.76        40.24        34.65        41.03        27.22 
TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN TCGA-S3-A6ZG 
       14.40        29.82        52.73        25.91        14.70        13.12 
TCGA-Z7-A8R5 
      108.07 

$`4P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        75.55        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       21.67        49.48        18.61        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
       53.06        29.03        31.00        26.01         1.02        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99        24.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       31.00         0.99        43.00        40.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       50.04        49.05        45.07        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD 
       19.04        13.02        21.04         0.99        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         5.72         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       14.99        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52         2.56        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
       73.64         5.26        86.66        42.35        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28        87.22        97.84        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        83.77        79.00        89.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       54.21        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       140.88       211.56       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
       73.51       139.17       170.17        85.35        74.99        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        59.84        20.45        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       23.44        38.01        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       20.12        90.84        72.56        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       82.85        42.28        12.00        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.66       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59        72.07        28.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
        8.94        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V 
       11.28         0.16        12.03        10.42         2.30         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.50        12.20         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        18.71        15.78        18.90 
TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        15.55        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        12.66        16.54        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       14.43         9.44        16.41         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       12.10        43.00        34.42        27.52        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        18.51        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
        8.75        43.04        16.93         5.52        15.72        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        26.56        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        13.48        12.00        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         6.12         3.02        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       32.09         1.12         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       12.89        23.51        20.71        17.06         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56         0.72        29.72         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41        30.18        15.72        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        13.81        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        55.00        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       79.10        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95        25.05        17.06        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       16.50        16.93        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       107.05 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.33              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           112.08            234.28 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            25.55             24.43 
[1] "0.3 - 112.1 (25.6)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3        3        1        1        31        15
  4P GAIN WILD-TYPE      86       78        7        2       322       230
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0         10          5          4        2
  4P GAIN WILD-TYPE         2        140         24         59       18
                   vv
clus                STAGE TIS STAGE X
  4P GAIN MUTATED           0       0
  4P GAIN WILD-TYPE         1      13
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 3                78
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA               31               322
  STAGE IIB               15               230
  STAGE III                0                 2
  STAGE IIIA              10               140
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    13  45  11   6
  4P GAIN WILD-TYPE 259 571 119  34
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               259
  T2              45               571
  T3              11               119
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    37  26   5   5
  4P GAIN WILD-TYPE 464 324 112  70
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              37               464
  N1              26               324
  N2               5               112
  N3               5                70
[1] 4 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    67   2
  4P GAIN WILD-TYPE 812  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     67    2
  4P GAIN WILD-TYPE  812   19
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              67               812
  1               2                19
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    74   1
  4P GAIN WILD-TYPE 977  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     74    1
  4P GAIN WILD-TYPE  977   10
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              74               977
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P GAIN MUTATED                            0                            58
  4P GAIN WILD-TYPE                          1                           705
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P GAIN MUTATED                                4                   1
  4P GAIN WILD-TYPE                            188                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P GAIN MUTATED                       0                                3
  4P GAIN WILD-TYPE                     4                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4P GAIN MUTATED                    1              8
  4P GAIN WILD-TYPE                 16             40
D7V8, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 58               705
  INFILTRATING LOBULAR CARCINOMA                 4               188
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19  56
  4P GAIN WILD-TYPE 269 718
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19   56
  4P GAIN WILD-TYPE  269  718
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               19               269
  YES              56               718
[1] 2 2
[1] FALSE
D7V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                1    58
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           8    51
  4P GAIN WILD-TYPE                       162   685
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                58
  BLACK OR AFRICAN AMERICAN                      8               162
  WHITE                                         51               685
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  58
  4P GAIN WILD-TYPE  35 800
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   58
  4P GAIN WILD-TYPE   35  800
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                35
  NOT HISPANIC OR LATINO              58               800
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    60  10
  4Q GAIN WILD-TYPE 856 118
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               70               974 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               118 
$`4Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        49.84        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A079 
       20.25        26.96        13.74        13.02        29.03         9.01 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
       18.97         9.99        19.96        33.01       112.08        33.01 
TCGA-A8-A0A9 TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0J3 
       27.02         2.27        16.57         1.78         0.33        21.40 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A250 TCGA-AR-A2LL TCGA-B6-A0RG 
       32.91        74.79        98.93        89.00        66.15        68.45 
TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N 
       24.53        25.55        22.13        27.25        26.66        37.74 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FC TCGA-BH-A1FM TCGA-D8-A1J8 TCGA-D8-A1JD 
       55.69        49.58       114.15        45.63        14.17        18.15 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XZ 
       12.03        14.01        13.32        27.58        15.22        15.32 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14S TCGA-E2-A152 
       13.48        10.09        12.26        46.59        33.17        27.12 
TCGA-E2-A15E TCGA-E2-A15O TCGA-E2-A1LA TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE 
       20.71        13.02        24.59         2.76        40.24        34.65 
TCGA-E9-A247 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN 
       27.22        14.40        29.82        52.73        25.91        14.70 
TCGA-OL-A66I TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-Z7-A8R5 
       23.47        13.12        15.39       108.07 

$`4Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        75.55        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       21.67        49.48        18.61        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.93        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       17.98        53.06        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       53.98        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       38.01        28.96        33.01        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00        31.00         0.99        43.00        40.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       38.79        26.04        50.70        33.04         0.92        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
       16.31        14.83        22.19        14.99        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55        11.44        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25       108.72       106.78       108.03        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
        2.56        19.20       111.32        73.64         5.26        86.66 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       42.35        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       62.14        33.73       160.90        50.89        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        62.86        54.21        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       74.99        68.12       103.63        71.15        59.84        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        23.44        38.01        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY 
        2.50        13.61        36.85        12.89        51.32        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
        8.81         2.01         7.23        20.12        90.84        72.56 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.16        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       12.00        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        9.44        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16         2.24         1.87         1.12         1.05         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.08        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.50        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        18.71        15.78        18.90        12.03 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        18.15        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.83        14.50        19.92        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       47.15        44.68        40.96        38.24        38.60        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        28.60        18.51 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       25.41        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       25.05        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       27.42        39.62        19.66        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       15.72         8.28        30.61        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       12.85        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        6.12         3.02        21.21        32.09        32.09         1.12 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       12.53        13.32        39.09        22.75        41.03        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       23.51        20.71        17.06         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        15.72        12.33        23.84        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       13.81        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       19.96        55.00        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       23.51         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.43        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       25.05        17.06        15.32        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        14.73        14.07        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       86.96         0.16         0.26         9.93        16.50        16.93 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       16.80        13.84        15.35        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       17.03         3.81        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.33              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           114.15            234.28 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           24.560            24.525 
[1] "0.3 - 114.2 (24.6)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.6"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         4        4        2        0        29        14
  4Q GAIN WILD-TYPE      85       77        6        3       324       231
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          8          5          4        2
  4Q GAIN WILD-TYPE         2        142         24         59       18
                   vv
clus                STAGE TIS STAGE X
  4Q GAIN MUTATED           0       0
  4Q GAIN WILD-TYPE         1      13
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  4                85
  STAGE IA                 4                77
  STAGE IB                 2                 6
  STAGE II                 0                 3
  STAGE IIA               29               324
  STAGE IIB               14               231
  STAGE III                0                 2
  STAGE IIIA               8               142
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    17  40   9   6
  4Q GAIN WILD-TYPE 255 576 121  34
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              17               255
  T2              40               576
  T3               9               121
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    34  27   4   5
  4Q GAIN WILD-TYPE 467 323 113  70
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              34               467
  N1              27               323
  N2               4               113
  N3               5                70
[1] 4 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    64   2
  4Q GAIN WILD-TYPE 815  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     64    2
  4Q GAIN WILD-TYPE  815   19
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              64               815
  1               2                19
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    71   1
  4Q GAIN WILD-TYPE 980  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     71    1
  4Q GAIN WILD-TYPE  980   10
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              71               980
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q GAIN MUTATED                            0                            56
  4Q GAIN WILD-TYPE                          1                           707
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q GAIN MUTATED                                4                   2
  4Q GAIN WILD-TYPE                            188                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q GAIN MUTATED                       0                                2
  4Q GAIN WILD-TYPE                     4                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4Q GAIN MUTATED                    1              7
  4Q GAIN WILD-TYPE                 16             41
D8V8, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 56               707
  INFILTRATING LOBULAR CARCINOMA                 4               188
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                28
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 7                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    20  52
  4Q GAIN WILD-TYPE 268 722
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     20   52
  4Q GAIN WILD-TYPE  268  722
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               20               268
  YES              52               722
[1] 2 2
[1] FALSE
D8V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                1    59
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                          10    48
  4Q GAIN WILD-TYPE                       160   688
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                59
  BLACK OR AFRICAN AMERICAN                     10               160
  WHITE                                         48               688
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  56
  4Q GAIN WILD-TYPE  35 802
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   56
  4Q GAIN WILD-TYPE   35  802
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                35
  NOT HISPANIC OR LATINO              56               802
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   271  36
  5P GAIN WILD-TYPE 645  92
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              307               737 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36                92 
$`5P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04W 
      129.14       131.67        13.68        39.32        19.20       101.98 
TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       56.81       134.40        80.28        79.76        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0SW TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE 
       31.82        24.72        44.88        18.90        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B 
       21.90        23.77        17.36        60.72        20.25        42.44 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD 
       29.98        50.37        24.39        26.96        21.14        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J 
       30.61        33.11        29.79        31.73        25.15        20.61 
TCGA-A7-A2KD TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       22.32        14.70        14.93        13.74        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       14.73        12.10        10.29         9.37        10.42        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07U 
        1.02        17.98        29.03         1.02        18.97        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G 
        9.99        45.07        13.02        38.01        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       12.00        31.00         0.99        17.95        41.98        12.00 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09X 
        9.99        12.00         1.02        25.02         8.98        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2QJ 
       12.00        13.02        27.02         2.37        10.85         2.27 
TCGA-AC-A3HN TCGA-AC-A62V TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03Y 
       16.31        11.44         0.03        20.19         1.12         0.33 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FJ TCGA-AN-A0FK 
        1.78         9.96         0.16         0.33         7.96         7.00 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XU TCGA-AO-A03L 
        0.33         0.33         0.33        12.33         0.33        80.28 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 
       61.35        81.63        32.78        21.40        20.32        53.03 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       50.86        76.77        55.33        71.80       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A0Y5 
       98.27        57.30        70.39         0.53        24.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A1AI TCGA-AR-A1AK 
        2.56        32.91         5.26        42.35        61.84        51.25 
TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       61.28        33.73        87.22        53.36        85.35        50.96 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       72.76        58.92        54.21        66.15        20.38        54.74 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0WV TCGA-B6-A0WY 
       20.45        77.62       176.98       140.88        79.63       113.79 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       73.51        68.12       103.63        24.53        59.84        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF 
       28.50        39.55        48.36        56.98        37.22        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP 
       21.70        44.05        48.69        44.02        22.13        15.65 
TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HP 
        2.56        24.49        31.00        24.43        23.08        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K 
       36.85        27.25        50.79        42.35        44.81        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       26.66        72.56        37.74        51.39        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FM 
       42.28        12.00        55.69        31.53        97.48        45.63 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A6R9 
       26.14        38.60        57.83        20.12         9.63         5.26 
TCGA-BH-A8FY TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A135 
        9.70        11.93        11.77        12.66         3.16         1.05 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A146 
       11.28        12.03         2.30         0.99        13.97        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       14.17        17.49        18.90        12.03        14.01        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       20.12        20.09        13.32        17.79        27.58        18.15 
TCGA-D8-A1XL TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       19.92        16.31        12.99        12.66        16.54        15.52 
TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X 
       14.24        13.05        14.43        12.53        12.26        12.10 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T 
       34.42        37.51        44.68        40.96        33.17        33.30 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 
       28.60        18.51        27.12        23.24        21.04        14.79 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B4 
       20.71        18.21        20.58        11.05        53.62        33.01 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IU 
       32.35        17.10        33.73        33.70        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A574 
       54.18        19.66        18.87       106.75        16.93        26.56 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 
       12.85        13.48        36.56         9.86         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02         2.76        21.21        32.09        40.24         1.12 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A243 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO 
       21.27        34.59        17.06         7.13         0.72        26.07 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 
       12.33        23.84         0.79        14.40         8.48        16.57 
TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A423 
       28.77        29.82        23.11         6.15        13.94        10.16 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV TCGA-HN-A2OB 
       83.34        72.10       110.50        66.38        13.55        62.43 
TCGA-LD-A66U TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       21.24        15.32        14.79         2.63        14.73        14.07 
TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE 
       22.39        20.38        26.04         8.91        47.01        86.96 
TCGA-PL-A8LX TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UU-A93S TCGA-W8-A86G TCGA-Z7-A8R5 
        0.16        13.12        16.93         3.81        11.41       108.07 
TCGA-Z7-A8R6 
      107.05 

$`5P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        31.79         7.96        28.01        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       98.99       107.93        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       25.22       101.72       107.61        74.40        72.00        61.94 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       32.55        25.28        50.47        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G1 
       19.33        48.46        31.73        23.47        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
      105.34        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW 
       32.75        49.48        47.31        34.98        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.30        23.21        21.90        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       37.45        35.67        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        23.80        21.73        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SE TCGA-A7-A5ZW 
       10.29        11.28        13.41        11.97        21.17        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       11.05         8.75        13.02        53.06        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
        7.99        18.05        15.06        36.95         0.99        28.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       37.05         9.99        31.00        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09E 
       40.01        33.01        30.97         9.99        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V 
       45.07        29.98        33.07         1.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD 
        0.99        19.04        21.04         0.99        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.92        32.45        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
       18.67        13.58        12.26         1.68         8.22         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         6.51         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        5.65         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.36         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        72.00        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       50.24        62.04       102.58        99.25       108.72       108.03 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       61.87        17.79        26.93       130.09        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
       19.20       111.32        73.64        74.79        86.66        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        75.55        52.77        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       76.21        63.62        62.14       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       96.89        78.51        84.20         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       76.01        83.77        79.00        89.00        78.48        73.18 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       143.21        20.25        62.86        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 
       39.39        40.54        16.04        10.59       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      131.21       157.41        97.48       188.68        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52       139.17       170.17        85.35        74.99 
TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 
       71.15        25.55        46.95        40.83        39.16        56.94 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO 
       51.68        32.02        18.21        24.85        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        13.91        48.23        17.26         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY 
       14.30         9.63        44.81        46.19        32.58        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HU 
       52.96        26.50        20.38         5.85         2.50        12.89 
TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F 
       51.32         5.59        23.93        24.95        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
        2.01         7.23        20.12        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX 
       66.05         7.36        51.16       113.82        82.85        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       17.69        25.81        89.16        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 
       72.07       144.59        72.07        28.14        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       10.65         6.44        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
       23.51        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        2.24         1.87         1.12         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       10.92        11.34         0.16        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.50        12.20         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        14.17        13.48        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN 
       15.78        18.15        12.03        18.97        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        14.70        18.58        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       14.50        17.69        15.55        16.41        15.85         6.35 
TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.16        15.32         9.93        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       13.45         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       10.09        13.08        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
        8.02        43.00        27.52        46.59        40.41        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U 
       28.44        28.87        47.15        38.24        38.60        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A156 
       34.26        32.02        31.96        25.41        19.43        23.87 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H 
       25.05        23.34        22.82        17.29        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       17.42        19.40         9.04        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.07        14.99        60.53        53.03        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       20.98        27.42        39.62        24.59        40.47        28.90 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        34.29        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A1RE 
       25.84        11.90        28.27        34.95        32.09        34.65 
TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        22.75        41.03        12.89        23.51        20.71 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
        0.69        27.22         1.94        24.56        29.72         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       18.41        30.18        15.72        14.70        13.81        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       12.20        39.72        18.21        18.90        13.25        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       19.99        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       52.73        25.91        22.09        34.03        17.49        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
        7.40       109.87        59.57       216.76        79.10        75.02 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PX 
       85.35        38.20        43.73        69.30        72.03        18.12 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
        2.60        11.84        11.57        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.70        14.47        22.26        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.50        14.70        12.36        27.91         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       41.92        42.77        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       40.11        64.21         0.26         9.93        16.50        16.80 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       15.39        13.84        15.35        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03        52.96        29.03        15.35        16.04 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           176.98            234.28 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            21.24             25.81 
[1] "0.0 - 177.0 (21.2)" "0.0 - 234.3 (25.8)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED        29       18        1        1       110        67
  5P GAIN WILD-TYPE      60       63        7        2       243       178
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           1         49          9         16        6
  5P GAIN WILD-TYPE         1        101         20         47       14
                   vv
clus                STAGE TIS STAGE X
  5P GAIN MUTATED           0       3
  5P GAIN WILD-TYPE         1      10
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 29                60
  STAGE IA                18                63
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA              110               243
  STAGE IIB               67               178
  STAGE III                1                 1
  STAGE IIIA              49               101
  STAGE IIIB               9                20
  STAGE IIIC              16                47
  STAGE IV                 6                14
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    73 181  43  13
  5P GAIN WILD-TYPE 199 435  87  27
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              73               199
  T2             181               435
  T3              43                87
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED   161  84  44  17
  5P GAIN WILD-TYPE 340 266  73  58
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             161               340
  N1              84               266
  N2              44                73
  N3              17                58
[1] 4 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   271   6
  5P GAIN WILD-TYPE 608  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    271    6
  5P GAIN WILD-TYPE  608   15
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             271               608
  1               6                15
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   306   5
  5P GAIN WILD-TYPE 745   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    306    5
  5P GAIN WILD-TYPE  745    6
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             306               745
  MALE                 5                 6
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P GAIN MUTATED                            1                           227
  5P GAIN WILD-TYPE                          0                           536
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P GAIN MUTATED                               55                   2
  5P GAIN WILD-TYPE                            137                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P GAIN MUTATED                       3                                7
  5P GAIN WILD-TYPE                     1                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5P GAIN MUTATED                    2             14
  5P GAIN WILD-TYPE                 15             34
D9V8, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                227               536
  INFILTRATING LOBULAR CARCINOMA                55               137
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                14                34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    93 218
  5P GAIN WILD-TYPE 195 556
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     93  218
  5P GAIN WILD-TYPE  195  556
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               93               195
  YES             218               556
[1] 2 2
[1] FALSE
D9V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    11
  5P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          44   220
  5P GAIN WILD-TYPE                       126   516
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     44               126
  WHITE                                        220               516
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    10 250
  5P GAIN WILD-TYPE  28 608
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10  250
  5P GAIN WILD-TYPE   28  608
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                28
  NOT HISPANIC OR LATINO             250               608
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   186  20
  5Q GAIN WILD-TYPE 730 108
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              206               838 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               108 
$`5Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0ET 
      129.14        13.68        39.32        56.81       134.40        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG 
       34.29        31.82        18.90        20.75        18.21        21.90 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A3XU TCGA-A2-A4RX TCGA-A2-A4S1 
       17.36        60.72        20.25        29.98        24.39        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J 
       21.14        38.30        33.11        29.79        25.15        20.61 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q 
       14.70        13.74        14.50        10.29        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 
       17.98         1.02        18.97         9.99        45.07        13.02 
TCGA-A8-A08G TCGA-A8-A08R TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09B 
       19.96         0.99        17.95        41.98        12.00        12.00 
TCGA-A8-A09C TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 
        1.02         8.98        14.01        12.00        13.02        27.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A7VC TCGA-AC-A8OP 
        2.37        10.85         2.27        16.31         0.03        20.19 
TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FX 
        0.33         9.96         0.16         0.33         7.00         0.33 
TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 
       12.33        80.28        81.63        32.78        20.32        53.03 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       50.86        76.77        71.80        90.58        98.27        57.30 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV 
        0.53         5.65         5.26        61.84        51.25        61.28 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK 
       87.22        85.35        50.96        72.76        58.92        54.21 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KI 
       66.15        54.74        20.45        79.63       113.79        73.51 
TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B7 
       68.12       103.63        24.53        28.50        48.36        56.98 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP 
       37.22        21.70        44.05        44.02        22.13        15.65 
TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0HQ TCGA-BH-A0HX 
        2.56        24.49        31.00        23.08        36.85        27.25 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       42.35        44.81        90.84        26.66        72.56        37.74 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A202 
       51.39        69.93        91.99        42.28        97.48        26.14 
TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-C8-A12P TCGA-C8-A135 
       20.12         9.63         5.26         9.70        11.77         1.05 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JE 
       11.34        11.28        12.03        21.14        14.17        18.90 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       14.01        20.09        13.32        17.79        27.58        18.15 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27I 
       16.31        12.99        16.54        15.52        14.24        14.43 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O 
       12.53        12.26        12.10        34.42        37.51        44.68 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15G 
       33.17        33.30        27.12        23.24        20.71        18.21 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1IU 
       33.01        32.35        17.10        33.73        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E2-A9RU 
       54.18        19.66        18.87       106.75         8.28        12.85 
TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       13.48         9.86         2.56         6.12         3.02         2.76 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS 
       40.24         1.12        21.27         7.13         0.72        29.72 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 
       12.33         0.79        14.40         8.48        16.57        28.77 
TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A3NW TCGA-GM-A3XN 
       23.11         6.15        10.16        83.34       110.50        66.38 
TCGA-GM-A5PV TCGA-LD-A66U TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
       13.55        21.24         2.63        14.73        14.07        22.39 
TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-W8-A86G 
       26.04         8.91        86.96        13.12        16.93        11.41 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

$`5Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       75.55        75.25         5.19        98.99       107.93        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       34.55        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
      107.61        79.76        74.40        72.00        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       17.46        32.55        25.28        50.47        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        83.01        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        50.37        38.37         7.30        21.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.67        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
        9.37        10.42         8.75        13.02        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A084 
       10.98         8.98         7.99        24.99        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       36.95         0.99        38.01        28.96        33.01        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00        31.00        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        33.01        30.97         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 
       25.02        19.04        15.02         0.99        19.04        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        17.03        38.04         0.95         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD 
       26.04        50.70        33.04         0.92        32.45        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         6.51         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.96         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        61.35        66.77        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        72.00        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      106.78       108.03        64.04        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93       130.09        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       111.32        73.64        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL 
       83.87       114.02        85.97        75.55        52.77        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       76.11        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        76.21        63.62        62.14        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
      104.28        97.84        76.01        53.36        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       89.00        78.48        73.18        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       62.86        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        10.59        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      220.90       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       89.46       131.21       157.41        97.48       188.68        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       58.88        43.59       101.52       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 
       74.99        71.15        59.84        20.45        25.55        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC 
       40.83        39.55        39.16        56.94        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        25.71        24.85        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        13.91        48.23        17.26         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI 
       14.30         9.63        44.81        46.19        32.58        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       13.61        12.89        51.32        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V 
       30.28        55.63        37.55        66.05         7.36        51.16 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       45.63        72.07       144.59        72.07        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T 
       83.31        57.83       130.16        10.65         6.44        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 
      109.28         8.94        18.64        23.51        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        2.24         1.87         1.12         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       10.92         0.16        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.50        12.20         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       13.25        20.58        13.97        14.17        13.48        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF 
       17.49        16.50        18.71        15.78        18.15        12.03 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       12.03        18.97        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        14.70        18.58        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        15.55        16.41        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
        6.35        15.16        12.66        15.32         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.45        13.05         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 
       13.48         4.80         0.76        10.09        13.08        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 
       18.51        21.67        16.18         8.02        43.00        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        40.11        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       40.96        38.24        38.60        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 
       31.96        28.60        18.51        25.41        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       60.53        53.62        53.03        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.70        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       20.98        27.42        39.62        24.59        40.47        28.90 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        26.56        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        35.24        25.84        11.90        28.27        34.95 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       21.21        32.09        32.09        34.65         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       22.75        41.03        12.89        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69        27.22         1.94        24.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
       18.41        30.18        15.72        23.84        14.70        13.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       15.39        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       34.03        17.49        23.51         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY 
       86.96       115.69       106.06       101.62        85.35        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       43.73        69.30        72.03        18.12         2.60        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        14.79        22.26        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        7.46        14.50        14.70        12.36        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        41.92        42.77        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       28.21        19.73        40.11        47.01        64.21         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        16.50        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       52.96        29.03        15.35        16.04 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           134.40            234.28 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            20.66             25.25 
[1] "0.0 - 134.4 (20.7)" "0.0 - 234.3 (25.2)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED        19       16        0        1        67        48
  5Q GAIN WILD-TYPE      70       65        8        2       286       197
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1         35          5         13        1
  5Q GAIN WILD-TYPE         1        115         24         50       19
                   vv
clus                STAGE TIS STAGE X
  5Q GAIN MUTATED           0       2
  5Q GAIN WILD-TYPE         1      11
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                16                65
  STAGE IB                 0                 8
  STAGE II                 1                 2
  STAGE IIA               67               286
  STAGE IIB               48               197
  STAGE III                1                 1
  STAGE IIIA              35               115
  STAGE IIIB               5                24
  STAGE IIIC              13                50
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    54 112  35   7
  5Q GAIN WILD-TYPE 218 504  95  33
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              54               218
  T2             112               504
  T3              35                95
  T4               7                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED   107  58  28  13
  5Q GAIN WILD-TYPE 394 292  89  62
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0             107               394
  N1              58               292
  N2              28                89
  N3              13                62
[1] 4 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   179   1
  5Q GAIN WILD-TYPE 700  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    179    1
  5Q GAIN WILD-TYPE  700   20
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             179               700
  1               1                20
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   207   2
  5Q GAIN WILD-TYPE 844   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    207    2
  5Q GAIN WILD-TYPE  844    9
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE             207               844
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q GAIN MUTATED                            0                           140
  5Q GAIN WILD-TYPE                          1                           623
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q GAIN MUTATED                               46                   1
  5Q GAIN WILD-TYPE                            146                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q GAIN MUTATED                       3                                6
  5Q GAIN WILD-TYPE                     1                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5Q GAIN MUTATED                    2             11
  5Q GAIN WILD-TYPE                 15             37
D10V8, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                140               623
  INFILTRATING LOBULAR CARCINOMA                46               146
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          3                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                11                37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    63 146
  5Q GAIN WILD-TYPE 225 628
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     63  146
  5Q GAIN WILD-TYPE  225  628
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               63               225
  YES             146               628
[1] 2 2
[1] FALSE
D10V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     7
  5Q GAIN WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          19   159
  5Q GAIN WILD-TYPE                       151   577
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     19               151
  WHITE                                        159               577
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7 167
  5Q GAIN WILD-TYPE  31 691
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7  167
  5Q GAIN WILD-TYPE   31  691
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                31
  NOT HISPANIC OR LATINO             167               691
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED   177  28
  6P GAIN WILD-TYPE 739 100
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              205               839 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               28               100 
$`6P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A04X TCGA-A2-A0CM 
        9.96        31.79        28.01        73.84        55.43        24.79 
TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0T2 
       33.76        79.76        35.05        31.82        63.29         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX 
       18.21        21.90        18.61        31.73        23.77        60.72 
TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       17.19        33.93        32.75        47.31        34.98        38.37 
TCGA-A2-A4S1 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F 
       26.96        38.30        30.61        35.67        29.79        25.15 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       21.73        20.61        14.70        14.50        21.17        17.92 
TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F 
       10.29        17.98        31.00        17.03        53.98        18.97 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R 
        8.98        24.99         9.99        38.01        28.96         0.99 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-AC-A23E 
       33.01        30.97        12.00        49.05        25.02         2.37 
TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A03Y 
       33.04        16.57        13.71         0.03         1.12         0.33 
TCGA-AN-A041 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY 
        0.23         9.96         0.16         7.00         0.36         0.33 
TCGA-AN-A0XN TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JL TCGA-AO-A0JM 
        0.33        80.28        66.77        81.63        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A0Y5 
      102.58       108.03        98.27        48.36         0.53         5.65 
TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AV 
       19.20         5.26        74.79        42.35        65.36        61.28 
TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LL TCGA-AR-A2LR 
      104.28        79.00        89.00        58.92        66.15        20.38 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RU TCGA-B6-A0WY 
      143.38        12.13        84.59       110.14       131.21       113.79 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40C 
      186.48        43.59       101.52        74.99        68.12        71.15 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA 
       59.84        20.45        25.55        39.55        56.94        37.22 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DH 
       24.85        44.05        45.57        49.05        44.02        38.01 
TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18T 
       24.49        36.85        23.05        90.84        55.63         7.36 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A203 
       69.93        91.99        12.00        31.53       114.15        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12X 
       57.83       130.16         8.94        18.64        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 
        3.16         0.16         2.30         0.36        20.88        13.97 
TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK 
       14.17        14.17        20.09        20.09        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F 
       19.92        16.41        16.54        15.32        14.14        16.04 
TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A10C TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 
       10.09        12.53        40.11        31.96        18.51        25.41 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1IL 
       25.05        11.05        14.07        53.62        33.70         3.88 
TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A56Z 
       22.19        18.87       106.75       102.61        16.93         8.28 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1RF TCGA-E9-A295 
       34.92        26.56        13.12        12.59         6.58         0.72 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 
       26.07        30.18        23.84        25.94        22.82        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C9 
       18.48        30.08         7.86        25.91        10.16       109.87 
TCGA-GM-A2DF TCGA-HN-A2NL TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A6FR 
       70.85         2.60         7.10        11.44        14.70        16.08 
TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5S0 
       15.68        14.50        12.36        58.62        36.36        20.38 
TCGA-OL-A66I TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 
       23.47        86.96         9.93        16.50        16.80        15.39 
TCGA-Z7-A8R5 
      108.07 

$`6P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       104.81        18.02        78.41       121.94        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12       101.98        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       98.99       107.93        56.81        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72       134.40        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       72.00        34.29        61.94        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        50.43        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       25.28        50.47        21.67        49.48        19.33        48.46 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        17.36        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        42.44        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW 
       10.59        20.88        39.65        83.01        29.98        49.48 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.37         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.90        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        20.19        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D 
       11.28        13.41        11.97        14.93        13.74        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.02        13.02         1.02        53.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
        1.02         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z 
       12.00        32.05         9.99        10.98         7.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F 
       18.05        15.06        36.95        13.02         0.99        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       12.00         9.99         9.99         1.02        50.04        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
        0.99        27.02        17.03        38.04         0.95        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        5.72         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        26.04        50.70         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
       32.45        16.31        14.83        22.19        14.99        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR 
       13.58        12.26         1.68         8.22        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        2.30         0.33         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         7.36         6.51         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        7.04         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        61.35        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E 
       99.25       108.72       106.78        90.58        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93       130.09        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TW 
        2.56        32.91       111.32        73.64        86.66        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       76.11        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        76.21        63.62        62.14        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       87.22        97.84        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       83.77        78.48        73.18        72.76        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        62.86        54.21        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       176.98        18.77       126.12       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI 
      129.57       129.70        28.27        68.94        58.88        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ 
      139.17       170.17        85.35       103.63        24.53        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       44.81         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       72.56        37.74        30.28        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16       113.82        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        89.16        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        9.44        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         0.39         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.12         1.05         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        11.28        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.50        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        11.90        13.25        20.58 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        19.20        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.97        20.12        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       14.73        17.69        15.55        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        15.16        12.66        15.52         9.93        14.24 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
       13.48         4.80         0.76        13.08        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y 
       33.17        33.30        43.33        34.26        32.02        28.60 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       12.92        17.42        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        60.53        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU 
       32.78        33.73        28.44        22.65        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       28.90         8.75        43.04         5.52        15.72        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       12.00        36.56        39.55        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        34.65        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       12.89        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        1.94         7.13        24.56        29.72         0.76        18.41 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       15.72        12.33        14.70         0.79        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PA 
       40.41        41.13        39.78        52.96        23.11        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       23.51         7.40        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95        25.05        17.06        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       22.26         2.63         7.46        14.70        14.73        14.07 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       40.08        34.92        28.87        24.72        22.32        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 
        0.16         0.26        13.12        16.93        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       107.05 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.03              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           186.48            234.28 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            24.99             24.39 
[1] "0.0 - 186.5 (25.0)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED        15        9        2        0        80        50
  6P GAIN WILD-TYPE      74       72        6        3       273       195
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         26          7         10        4
  6P GAIN WILD-TYPE         2        124         22         53       16
                   vv
clus                STAGE TIS STAGE X
  6P GAIN MUTATED           0       1
  6P GAIN WILD-TYPE         1      12
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                 9                72
  STAGE IB                 2                 6
  STAGE II                 0                 3
  STAGE IIA               80               273
  STAGE IIB               50               195
  STAGE III                0                 2
  STAGE IIIA              26               124
  STAGE IIIB               7                22
  STAGE IIIC              10                53
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    39 134  25   7
  6P GAIN WILD-TYPE 233 482 105  33
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              39               233
  T2             134               482
  T3              25               105
  T4               7                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED   102  62  25  11
  6P GAIN WILD-TYPE 399 288  92  64
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0             102               399
  N1              62               288
  N2              25                92
  N3              11                64
[1] 4 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   170   4
  6P GAIN WILD-TYPE 709  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    170    4
  6P GAIN WILD-TYPE  709   17
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             170               709
  1               4                17
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   204   1
  6P GAIN WILD-TYPE 847  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    204    1
  6P GAIN WILD-TYPE  847   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE             204               847
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P GAIN MUTATED                            0                           164
  6P GAIN WILD-TYPE                          1                           599
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P GAIN MUTATED                               19                   4
  6P GAIN WILD-TYPE                            173                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P GAIN MUTATED                       1                                3
  6P GAIN WILD-TYPE                     3                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6P GAIN MUTATED                    1             12
  6P GAIN WILD-TYPE                 16             36
D11V8, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                164               599
  INFILTRATING LOBULAR CARCINOMA                19               173
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                12                36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    63 142
  6P GAIN WILD-TYPE 225 632
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     63  142
  6P GAIN WILD-TYPE  225  632
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               63               225
  YES             142               632
[1] 2 2
[1] FALSE
D11V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     8
  6P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          46   132
  6P GAIN WILD-TYPE                       124   604
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     46               124
  WHITE                                        132               604
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9 161
  6P GAIN WILD-TYPE  29 697
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  161
  6P GAIN WILD-TYPE   29  697
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                29
  NOT HISPANIC OR LATINO             161               697
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED   127  20
  6Q GAIN WILD-TYPE 789 108
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              147               897 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               108 
$`6Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 
       13.68        31.79        19.20        55.43        24.79        33.76 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        63.29         8.38        18.21        21.90        18.61 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CD 
       60.72        19.20        47.31        34.98        26.96        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       30.61        35.67        29.79        14.70        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07F 
       17.92        10.29        17.98        31.00        17.03        18.97 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A09B 
        8.98        38.01        28.96         0.99        33.01        12.00 
TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62X TCGA-AC-A7VC TCGA-AN-A03Y 
       25.02         2.37        33.04        13.71         0.03         0.33 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AO-A03O TCGA-AO-A124 TCGA-AO-A129 
        0.16         7.00         0.33        81.63       102.58       108.03 
TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TS 
       98.27        48.36         0.53         5.65        19.20        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AV TCGA-AR-A24Q 
       86.66        42.35        65.36        61.84        61.28       104.28 
TCGA-AR-A24Z TCGA-AR-A2LL TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IO 
       79.00        66.15        20.38       143.38        12.13       110.14 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA 
       74.99        59.84        25.55        39.55        56.94        37.22 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB 
       24.85        44.05        45.57        49.05        44.02        24.49 
TCGA-BH-A0HQ TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A203 
       36.85        55.63        91.99        12.00        31.53        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L 
       57.83       130.16         8.94        18.64        23.51        11.93 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z 
       12.66         3.16         0.16         2.30         0.36        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JP 
       13.97        14.17        14.17        20.09        20.09        21.01 
TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XY TCGA-D8-A1XZ 
       18.58        21.83        14.50        16.41        16.54        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27V TCGA-E2-A10C TCGA-E2-A14X TCGA-E2-A14Z 
       14.14        16.04        12.53        40.11        31.96        18.51 
TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1LH 
       25.41        25.05        11.05        53.62        33.70       106.75 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A3QA 
       16.93        34.92        26.56        13.12        35.24        30.18 
TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       23.84        25.94        29.82        18.48        30.08         7.86 
TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-HN-A2NL TCGA-LD-A7W5 TCGA-LL-A5YN 
       10.16       109.87        72.10         2.60         7.10        14.70 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 TCGA-OL-A5DA TCGA-PE-A5DE TCGA-PL-A8LZ 
       16.08        15.68        12.36        58.62        86.96         9.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-Z7-A8R5 
       16.80        15.39       108.07 

$`6Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        20.88         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       87.25        63.12       101.98        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52        17.13        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       49.48        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       37.45        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A5ZV 
       13.41        11.97        14.93        13.74        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        53.06        29.03        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        45.07        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
        0.99        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00        31.00       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        50.70         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55        11.44        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
       12.26         1.68         8.22        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        1.78         1.71         9.96         7.36         6.51         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         6.44         5.65         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         7.04         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       55.33        71.80        99.25       108.72       106.78        90.58 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52         2.56        32.91       111.32        73.64 
TCGA-AR-A0TR TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
        5.26        98.93        64.83        55.86       107.24       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK 
       83.87       114.02        85.97        75.55        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        76.21        63.62        62.14        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76        87.22        97.84        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        89.00        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       143.21        20.25        62.86        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       52.11        38.17        39.39        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       20.45        10.59        77.62       149.59       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ 
       68.12       103.63        71.15        24.53        20.45        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       26.50        20.38         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         0.39         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       11.28        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       12.20         0.99         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
       13.41        19.46        11.90        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.12        19.40        20.38        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM 
       12.39        17.16        15.22        14.73        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       15.55        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       12.66        15.52         9.93        14.24        17.42        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        10.09        13.08        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 
       33.30        43.33        34.26        32.02        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       23.24        19.43        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P 
       17.42        19.40         9.04        20.58        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        60.53        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        40.47        28.90        18.87       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       43.04         5.52        15.72         8.28        30.61        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       12.85        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       36.56        39.55        12.59        35.77        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       12.89        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       26.07        18.41        15.72        12.33        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       13.81        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       52.96        23.11        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 
       25.91        22.09        34.03        17.49        23.51         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       13.22        13.28        10.62        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       25.05        17.06        15.32        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
        2.63         7.46        14.50        14.70        14.73        14.07 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF 
        8.91        47.01        64.21         0.16         0.26        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       13.12        16.93        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.03              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           143.38            234.28 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            24.49             24.56 
[1] "0.0 - 143.4 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED        12        7        2        0        60        33
  6Q GAIN WILD-TYPE      77       74        6        3       293       212
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           0         17          5          8        2
  6Q GAIN WILD-TYPE         2        133         24         55       18
                   vv
clus                STAGE TIS STAGE X
  6Q GAIN MUTATED           0       0
  6Q GAIN WILD-TYPE         1      13
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 7                74
  STAGE IB                 2                 6
  STAGE II                 0                 3
  STAGE IIA               60               293
  STAGE IIB               33               212
  STAGE III                0                 2
  STAGE IIIA              17               133
  STAGE IIIB               5                24
  STAGE IIIC               8                55
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    26  96  20   5
  6Q GAIN WILD-TYPE 246 520 110  35
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              26               246
  T2              96               520
  T3              20               110
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    84  38  15   9
  6Q GAIN WILD-TYPE 417 312 102  66
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              84               417
  N1              38               312
  N2              15               102
  N3               9                66
[1] 4 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   125   2
  6Q GAIN WILD-TYPE 754  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    125    2
  6Q GAIN WILD-TYPE  754   19
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0             125               754
  1               2                19
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED   146   1
  6Q GAIN WILD-TYPE 905  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    146    1
  6Q GAIN WILD-TYPE  905   10
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE             146               905
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q GAIN MUTATED                            0                           117
  6Q GAIN WILD-TYPE                          1                           646
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q GAIN MUTATED                               13                   4
  6Q GAIN WILD-TYPE                            179                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q GAIN MUTATED                       1                                3
  6Q GAIN WILD-TYPE                     3                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6Q GAIN MUTATED                    1              8
  6Q GAIN WILD-TYPE                 16             40
D12V8, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                117               646
  INFILTRATING LOBULAR CARCINOMA                13               179
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    44 103
  6Q GAIN WILD-TYPE 244 671
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     44  103
  6Q GAIN WILD-TYPE  244  671
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               44               244
  YES             103               671
[1] 2 2
[1] FALSE
D12V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     7
  6Q GAIN WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          31    95
  6Q GAIN WILD-TYPE                       139   641
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     31               139
  WHITE                                         95               641
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7 114
  6Q GAIN WILD-TYPE  31 744
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  114
  6Q GAIN WILD-TYPE   31  744
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                31
  NOT HISPANIC OR LATINO             114               744
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   268  37
  7P GAIN WILD-TYPE 648  91
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              305               739 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37                91 
$`7P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN 
      129.14       131.67        48.10        20.88        13.68        39.32 
TCGA-A2-A04W TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EV TCGA-A2-A0EY 
      101.98        98.99       107.93        67.33        31.82        63.29 
TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       44.88        17.13         8.38        18.21        21.90        18.61 
TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       23.47        20.25        19.56        42.44        33.93        83.01 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       50.37        26.96        35.31        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H 
       31.73        20.19        25.15        23.61        24.26        23.80 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        13.74        14.50        21.17        17.92        12.10 
TCGA-A7-A6VV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       10.29         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07U TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08P 
       53.98        18.97        24.99        28.96        19.96        31.00 
TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23G TCGA-AC-A23H 
       29.98        33.07        14.01        12.00        10.85         5.72 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO 
       26.04         2.27        16.57        11.44        17.42         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A049 TCGA-AN-A0AL 
        0.03        20.19         1.12         2.30         0.62         6.51 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J3 
        7.04         0.36         0.33         0.33        66.77        21.40 
TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 
       37.48        50.70        72.00        55.33       102.58        99.25 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KR 
      106.78        98.27        64.04        57.30        61.87        70.39 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0U0 TCGA-AR-A0U2 
       15.62        32.52        32.91         5.26        65.36        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24Q 
      114.02        17.23        61.28       160.90        50.89       104.28 
TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 
       50.96        89.00        20.38        54.74        20.45       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IM 
      149.59        12.13       129.57        50.70       112.37       126.12 
TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WZ 
       84.59       211.56       234.28       157.41        79.63       129.57 
TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B4 
       85.35        24.53        20.45        25.55        28.50        39.16 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ 
       37.22        21.70        44.05        48.69        45.57        49.05 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       44.02        45.83        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       38.47         4.41         9.63        46.19        32.58        24.49 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0RX 
       30.35        23.08        13.61        36.85        50.79         5.59 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV 
       44.81        90.84        51.16        69.93        91.99        12.00 
TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A5IZ 
       49.58        97.48        33.17        72.07        26.14        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q 
       23.51         9.63         5.26        11.93        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A26X TCGA-C8-A26Y 
       12.66         2.24         4.08        11.28         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 
        8.28         9.67         0.03        14.17        21.14        14.17 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X9 
       18.15        12.03        12.03        20.12        20.09        23.90 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ 
       15.22        19.92        15.85        12.99        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B 
        9.93         9.44        33.37        18.51        34.42        37.51 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       40.11        40.96        38.60        33.30        34.26        32.02 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D 
       27.12        23.24        19.43        25.05        23.34        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ 
       20.71        18.21        17.42        11.05        17.06        60.53 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L9 
       32.35        17.10        33.73        33.70        20.98        19.66 
TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       28.90       102.61        43.04         8.28        30.61        34.92 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF 
       12.85        34.82        12.00        13.12        12.59        35.24 
TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
       11.90         2.56         6.12        21.21        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       40.24        34.13        12.89        27.22         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 
        0.72        26.07        15.72        12.33         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 
       22.82        41.13        52.96        29.82        23.11         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC 
       18.90        19.99        10.16         7.40        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DL TCGA-GM-A3XN TCGA-HN-A2NL TCGA-JL-A3YW 
       75.02        70.85       115.69        66.38         2.60        11.84 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ 
       10.62        24.95        11.44        15.32        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW 
       16.08        14.50        14.07        58.52        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66P 
       28.87        22.32        26.70        41.92        26.04        14.07 
TCGA-OL-A6VO TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH 
       28.21         8.91        86.96         0.16        16.50        16.93 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        29.03 

$`7P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK 
        8.52        14.37        43.43        14.27        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X 
       78.41       121.94        73.84        87.25        63.12        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX 
       88.60       107.93        75.55        75.25         5.19        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW 
       49.48        19.33        48.46        31.73        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       60.72        22.45        19.20        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        49.48        47.31        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13H 
       38.30        34.29        35.47        30.61        29.79        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       31.36        23.74        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 
       13.02        13.02        53.06        29.03        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       33.01        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 
       33.01       112.08        40.01        33.01        30.97         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        49.05        45.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 
        8.98        19.04        15.02         0.99        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.37         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       36.99        38.79        50.70        33.04         0.92        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
       16.31        14.83        22.19        14.99        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79         1.55        13.71        18.67        13.58        12.26 
TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        8.22         1.32         0.33         0.33         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        2.96         1.78         1.71         9.96         7.36         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX 
        7.00         7.59         7.17         6.28         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        52.18        26.04        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       21.53        50.86        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12F 
       62.04        71.80       108.72       108.03        90.58        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       41.62        28.37        14.73        82.62         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       24.79        26.93       130.09         5.65         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32        73.64        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH 
       64.83        55.86       107.24       101.95        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       43.56        39.98        43.07        37.81        76.21        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       62.14        33.73        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76        87.22        97.84        76.01        53.36        85.35 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       83.77        79.00        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ 
       52.11        38.17        39.39        40.54        16.04        10.59 
TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       77.62       220.90        65.72       146.50       176.98        18.77 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      110.14       110.93       140.88        68.45       189.01        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       131.21        97.48       188.68        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 
       43.59       101.52        73.51       139.17       170.17        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0B2 
       68.12       103.63        71.15        59.84        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        48.36        56.94        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        25.71        24.85        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.69        53.95        49.94        11.67        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        67.86        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       44.81        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
        5.85         2.50        12.89        51.32        27.25        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05         7.36        51.39       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.12        10.52       109.28         8.94         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
       21.76         9.44        11.77        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         0.39         3.16         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        1.05         4.11        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
        9.53         0.03         9.50        12.20         0.99         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        13.97        13.48        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        18.71        15.78        18.90        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA 
       14.70        18.58        17.79        16.73        25.74        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       18.15        12.39        17.16        14.73        21.83        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        15.55        16.41        16.31         6.35        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       12.66        15.52        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        13.05        14.43        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 
        0.76        10.09        13.08        12.53        12.26        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       16.18         8.02        12.10        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       40.41        28.44        28.87        47.15        44.68        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       33.17        43.33        31.96        28.60        18.51        25.41 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H 
       21.04        23.87        14.79        22.82        21.63        12.92 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
       19.40         9.04        20.58        13.02        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.62        53.03        33.01        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       22.19        11.08        54.18        27.42        39.62        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        18.87       106.75         8.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       15.72        26.56        34.29        32.88        36.82        13.48 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 
       36.56        39.55        35.77        25.84         9.86        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       34.95         3.02         2.76         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        34.59        35.64        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        41.03        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.69         1.94        29.72         0.76        18.41        30.18 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 
       15.68        25.94        29.95        29.85        40.41        39.78 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       34.03        17.49        23.51       109.87        59.57       216.76 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        85.15        86.96       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        69.30        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        62.43        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       13.28        10.95        25.05        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79        15.68         7.46        14.70        12.36        14.73 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91        22.39         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L 
       40.08        24.72        20.38        23.47        65.62        42.77 
TCGA-OL-A66O TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY 
       17.36        19.73        40.11        47.01        64.21         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        13.12        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       14.96        13.84        52.96        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           234.28            220.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            23.80             24.72 
[1] "0.0 - 234.3 (23.8)" "0.0 - 220.9 (24.7)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        19       21        3        1       111        68
  7P GAIN WILD-TYPE      70       60        5        2       242       177
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           0         41          8         22        7
  7P GAIN WILD-TYPE         2        109         21         41       13
                   vv
clus                STAGE TIS STAGE X
  7P GAIN MUTATED           0       5
  7P GAIN WILD-TYPE         1       8
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                21                60
  STAGE IB                 3                 5
  STAGE II                 1                 2
  STAGE IIA              111               242
  STAGE IIB               68               177
  STAGE III                0                 2
  STAGE IIIA              41               109
  STAGE IIIB               8                21
  STAGE IIIC              22                41
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    72 181  39  13
  7P GAIN WILD-TYPE 200 435  91  27
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              72               200
  T2             181               435
  T3              39                91
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED   144  98  31  25
  7P GAIN WILD-TYPE 357 252  86  50
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             144               357
  N1              98               252
  N2              31                86
  N3              25                50
[1] 4 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   244   7
  7P GAIN WILD-TYPE 635  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    244    7
  7P GAIN WILD-TYPE  635   14
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             244               635
  1               7                14
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   300   7
  7P GAIN WILD-TYPE 751   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    300    7
  7P GAIN WILD-TYPE  751    4
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             300               751
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P GAIN MUTATED                            1                           236
  7P GAIN WILD-TYPE                          0                           527
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P GAIN MUTATED                               41                   1
  7P GAIN WILD-TYPE                            151                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P GAIN MUTATED                       2                                8
  7P GAIN WILD-TYPE                     2                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7P GAIN MUTATED                    2             16
  7P GAIN WILD-TYPE                 15             32
D13V8, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                236               527
  INFILTRATING LOBULAR CARCINOMA                41               151
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                16                32
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    91 216
  7P GAIN WILD-TYPE 197 558
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     91  216
  7P GAIN WILD-TYPE  197  558
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               91               197
  YES             216               558
[1] 2 2
[1] FALSE
D13V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1    16
  7P GAIN WILD-TYPE                                0    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          56   210
  7P GAIN WILD-TYPE                       114   526
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     56               114
  WHITE                                        210               526
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     9 247
  7P GAIN WILD-TYPE  29 611
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  247
  7P GAIN WILD-TYPE   29  611
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                29
  NOT HISPANIC OR LATINO             247               611
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   233  27
  7Q GAIN WILD-TYPE 683 101
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              260               784 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               27               101 
$`7Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W 
      129.14       131.67        48.10        20.88        39.32       101.98 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0EY 
       98.99       107.93        67.33        33.76        31.82        63.29 
TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV 
       44.88         8.38        18.21        21.90        18.61        23.47 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ 
       20.25        19.56        42.44        33.93        83.01        50.37 
TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       26.96        35.31        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A425 TCGA-A7-A4SB 
       20.19        25.15        23.61        24.26        14.70        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A8-A06Q 
       14.50        21.17        17.92        12.10        10.29         1.02 
TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       17.98        26.01        18.97        24.99         9.99        45.07 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        33.01        19.96        37.05        31.00         0.99 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        33.01        17.95        41.98         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM 
       33.07        25.02        14.01        10.85         5.72        26.04 
TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VC 
        2.27        16.57        13.71        17.42         1.68         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A0FL TCGA-AN-A0FW TCGA-AN-A0FY 
       20.19         1.12         2.30         7.59         0.36         0.33 
TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JD 
        0.33        66.77        32.78        52.18        37.48        72.00 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      102.58        99.25        98.27        64.04        57.30        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TR 
       61.87        70.39        15.62        32.52        32.91         5.26 
TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A256 
       61.84        17.23        61.28        50.89       104.28        93.83 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       39.39        20.38        54.74        20.45       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0RE TCGA-B6-A0RI 
       12.13       112.37       176.98       126.12       211.56       234.28 
TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
      157.41        79.63       129.57        85.35        74.99        24.53 
TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       20.45        39.16        37.22        21.70        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO 
       45.57        49.05        44.02        45.83        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 
       15.65         2.56        38.47         4.41         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A18K TCGA-BH-A18V 
       32.58        24.49        36.85         5.59        90.84        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-BH-A5IZ TCGA-BH-A6R8 
       69.93        91.99        49.58        97.48        18.64         9.63 
TCGA-BH-A6R9 TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A1HN 
        5.26        12.66        12.66         1.12        11.28         3.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A146 
        0.36         0.43         8.28         9.67         0.03        21.14 
TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL 
       14.17        18.15        12.03        12.03        20.12        20.09 
TCGA-D8-A1XF TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 
       15.22        16.54        15.32         9.93         9.44        33.37 
TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R 
       18.51        34.42        37.51        40.11        40.96        38.60 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 
       33.30        34.26        27.12        23.24        19.43        25.05 
TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15R 
       23.34        17.29        20.71        18.21        17.42        17.06 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A56Z 
       60.53        17.10        33.73        33.70        19.66         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N8 TCGA-E9-A1NC 
       30.61        34.92        12.85        34.82        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1QZ TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 
       12.59        11.90        32.09        32.09        40.24        34.13 
TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-E9-A54X 
       12.89        27.22         7.13         0.72        15.72        12.33 
TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 
        8.48        28.77        22.82        52.96        23.11         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC 
       18.90        19.99        10.16         7.40        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL TCGA-GM-A3XN TCGA-HN-A2NL TCGA-JL-A3YW 
       75.02        70.85        69.30        66.38         2.60        11.84 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ 
       10.62        24.95        11.44        15.32        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW 
       16.08        14.50        14.07        58.52        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO 
       28.87        22.32        26.70        41.92        26.04        28.21 
TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-UU-A93S 
        8.91        86.96         0.16        16.50        16.93         3.81 
TCGA-W8-A86G TCGA-WT-AB44 
       11.41        29.03 

$`7Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
        8.52        14.37        43.43        14.27        47.24        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        28.01        19.20        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       56.81        34.55        61.58        25.22       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        19.33        48.46        31.73        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        60.72        22.45        19.20        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       38.37         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC 
       21.90        38.30        34.29        35.47        30.61        29.79 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       11.97        14.93        14.73        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
       10.42         8.75        13.02        13.02        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       10.98         8.98         7.99        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       13.02         0.99        38.01        12.00         9.99        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 
       33.01       112.08        40.01        30.97        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 
        8.98        19.04        15.02         0.99        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        27.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         2.37         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70        33.04         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
       32.45        16.31        14.83        22.19        14.99        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79         1.55        11.44        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       12.26         8.22         1.32         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.00         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO 
        7.04         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        58.95        29.13        21.40        26.04        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12G TCGA-AO-A12H 
      108.72       106.78       108.03        90.58        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09         5.65         2.56        19.20       111.32        73.64 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       75.55        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       43.56        39.98        43.07        37.81        76.21        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        33.73       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       84.20         2.76        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       85.35        50.96        83.77        79.00        89.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        58.92       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        66.15        52.11        38.17        40.54        16.04 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       10.59        77.62       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      146.50        18.77        84.59       110.14       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       189.01        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS 
      102.77       140.48       100.70        89.46       131.21        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        18.35        21.47       113.79       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      139.17       170.17        68.12       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 
       25.55        28.50        46.95        40.83        39.55        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       24.85        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       49.94        11.67        41.75        48.13        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV 
       23.44        38.01        22.13        13.91         3.22        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE 
       47.41        16.27        15.68        14.30        44.81        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01         7.23        20.12        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28         8.94        23.51 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
        0.39         3.16         2.24         1.87         1.05         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.08        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A275 
       10.42         2.30         0.30         0.23         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50        12.20         0.99         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.71        15.78        18.90        14.01        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       18.15        12.39        17.16        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 
        6.35        12.99        15.16        12.66        15.52        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       12.53        12.26        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       43.00        27.52        46.59        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W 
       47.15        44.68        38.24        33.17        43.33        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 
       31.96        28.60        18.51        25.41        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       14.79        22.82        21.63        12.92        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        13.02        19.56        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 
        8.75        43.04        16.93         5.52        15.72        26.56 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.29        32.88        36.82        13.48        13.12        36.56 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        35.24        25.84         9.86        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD 
        2.56         6.12         3.02         2.76        21.21         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 
       34.65         6.58        21.27        34.59        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        41.03        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS 
       20.71        17.06         0.69         1.94        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41        30.18        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        13.81        14.40        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       29.95        29.85        40.41        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       34.03        17.49        23.51       109.87        59.57       216.76 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV 
       85.35       110.50        38.20        43.73        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        62.43        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       13.28        10.95        25.05        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79        15.68         7.46        14.70        12.36        14.73 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91        22.39         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L 
       40.08        24.72        20.38        23.47        65.62        42.77 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD 
       17.36        14.07        19.73        40.11        47.01        64.21 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        13.12        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-WT-AB41 
       15.35        14.96        13.84        13.94        17.03        52.96 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           234.28            220.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           24.740            24.495 
[1] "0.0 - 234.3 (24.7)" "0.0 - 220.9 (24.5)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        15       20        3        0        97        57
  7Q GAIN WILD-TYPE      74       61        5        3       256       188
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           0         30          9         20        7
  7Q GAIN WILD-TYPE         2        120         20         43       13
                   vv
clus                STAGE TIS STAGE X
  7Q GAIN MUTATED           0       3
  7Q GAIN WILD-TYPE         1      10
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                20                61
  STAGE IB                 3                 5
  STAGE II                 0                 3
  STAGE IIA               97               256
  STAGE IIB               57               188
  STAGE III                0                 2
  STAGE IIIA              30               120
  STAGE IIIB               9                20
  STAGE IIIC              20                43
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    62 153  30  15
  7Q GAIN WILD-TYPE 210 463 100  25
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              62               210
  T2             153               463
  T3              30               100
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED   127  79  25  23
  7Q GAIN WILD-TYPE 374 271  92  52
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             127               374
  N1              79               271
  N2              25                92
  N3              23                52
[1] 4 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   207   7
  7Q GAIN WILD-TYPE 672  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    207    7
  7Q GAIN WILD-TYPE  672   14
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             207               672
  1               7                14
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   257   5
  7Q GAIN WILD-TYPE 794   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    257    5
  7Q GAIN WILD-TYPE  794    6
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             257               794
  MALE                 5                 6
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q GAIN MUTATED                            1                           200
  7Q GAIN WILD-TYPE                          0                           563
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q GAIN MUTATED                               36                   2
  7Q GAIN WILD-TYPE                            156                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q GAIN MUTATED                       2                                6
  7Q GAIN WILD-TYPE                     2                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7Q GAIN MUTATED                    2             13
  7Q GAIN WILD-TYPE                 15             35
D14V8, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                200               563
  INFILTRATING LOBULAR CARCINOMA                36               156
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                13                35
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    69 193
  7Q GAIN WILD-TYPE 219 581
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     69  193
  7Q GAIN WILD-TYPE  219  581
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               69               219
  YES             193               581
[1] 2 2
[1] FALSE
D14V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0    14
  7Q GAIN WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          55   169
  7Q GAIN WILD-TYPE                       115   567
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                46
  BLACK OR AFRICAN AMERICAN                     55               115
  WHITE                                        169               567
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     7 209
  7Q GAIN WILD-TYPE  31 649
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  209
  7Q GAIN WILD-TYPE   31  649
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                31
  NOT HISPANIC OR LATINO             209               649
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   245  36
  8P GAIN WILD-TYPE 671  92
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              281               763 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               36                92 
$`8P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14       131.67         9.96        43.43        14.27        13.68 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
      104.81       121.94        24.79        75.25        98.99        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ER 
       67.33        33.76        61.58        80.28        79.76        74.40 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       27.12        44.88         8.38        17.46        18.90        20.75 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A259 TCGA-A2-A3XS 
       18.21        18.61        20.25        19.20        52.47        33.93 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       47.31        34.98        38.37        24.39        26.96        21.14 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26F 
       38.30        30.61        35.67        29.79        25.15        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       23.80        21.73        10.29        11.97        14.93        14.50 
TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Y TCGA-A8-A06Z 
       10.72        10.29        10.42         8.75        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A082 TCGA-A8-A086 
       53.98         9.01        43.00        18.97        18.05        13.02 
TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A 
       28.96         0.99       112.08        30.97        17.95         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A2 
       12.00         1.02        49.05        33.07        14.01        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FM 
       27.02        17.03         2.37        10.85        99.35        26.04 
TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6NO 
        2.27        23.24        11.44        13.71        13.58         1.68 
TCGA-AC-A7VC TCGA-AN-A03X TCGA-AN-A0AJ TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW 
        0.03         0.33         9.96         7.00         7.04         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J7 TCGA-AO-A0JI 
        0.33         0.33        68.75        47.87        20.32        50.24 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ 
      108.03        98.27        57.30        48.36        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0U0 TCGA-AR-A0U4 
        0.53        32.52         2.56        32.91        65.36        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R 
       75.55        61.84        43.07        33.73       104.28        87.22 
TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       97.84        50.96        78.48        72.76        58.92        93.83 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP 
       20.25        54.21        66.15        20.38        16.04        20.45 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0RE TCGA-B6-A0RH 
      149.59       220.90       129.57       112.37       211.56       189.01 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WX TCGA-B6-A0X1 
       81.17        78.02       102.77       157.41        21.47       186.48 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
       43.59       101.52       170.17        85.35        74.99        24.53 
TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG 
       20.45        39.55        39.16        37.22        18.21        24.85 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E1 
       49.05        44.02        15.65         2.56        38.47        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 
       14.30        44.81        30.35        10.78        15.16        24.56 
TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18L 
       26.50        36.85        12.89         5.59        44.81        26.66 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F5 
       91.99       113.82        42.28        12.00        49.58        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A202 
      120.62       114.15        74.73       122.89        45.63        26.14 
TCGA-BH-A204 TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V 
       83.31        23.51         9.63        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A26X TCGA-C8-A273 
       12.66        12.66         3.16         1.05         0.36         9.67 
TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JP 
        0.03        20.58        13.97        12.03        14.01        21.01 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL 
       14.70        17.79        18.15        15.22        14.50        19.92 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       12.99        12.66        16.54        15.32         9.93        14.14 
TCGA-D8-A27I TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14U 
       14.43        12.53        34.42        46.59        44.68        43.33 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D 
       28.60        27.12        19.43        14.79        25.05        17.29 
TCGA-E2-A15F TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IN 
       21.63        14.07        60.53        28.50        17.10        22.19 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NE 
       16.93        34.92        34.29        36.82        13.48        35.77 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
       34.95         2.56         2.76        32.09        32.09        40.24 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 
       12.53        22.75        23.51        17.06        27.22         0.72 
TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY 
       29.72        15.72        12.33        14.70        14.40         8.48 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB 
       18.90        28.77        41.13        23.11        18.48        19.99 
TCGA-EW-A1PC TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO TCGA-HN-A2NL 
        6.15        83.34        75.02        70.85        85.35         2.60 
TCGA-LL-A5YO TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-OL-A5D7 
       14.47        15.68         7.46        14.50        14.70        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VR 
       31.99        58.62        23.47        26.04        28.21        40.11 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 
       13.12        15.39        15.35        11.41        52.96 

$`8P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM 
       14.37        48.10        47.24        20.88        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        19.20        18.21        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EM 
       75.55         5.19       107.93        34.55        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      134.40       107.61        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX 
       61.94        24.72        63.29        99.19        54.64        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0YC 
       44.28        17.52        17.13        49.84        20.52        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       22.45        19.56        16.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15       105.34        10.59        20.88        39.65        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       29.98        32.75        49.48        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       23.21        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       23.74        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        14.70        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       12.10        11.05         9.37        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E 
       17.98        53.06        29.03        31.00        17.03        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
        8.98         7.99        24.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       36.95         0.99        38.01        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X 
       37.05         9.99        31.00        31.00        33.01        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D 
       40.01        33.01        41.98        12.00         9.99        50.04 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        12.00        13.02        21.04         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       38.04         0.95         5.72         1.48        38.53        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70        33.04         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       19.79        24.79         1.55        17.42        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03Y 
        8.22        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.28 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03U 
       80.28        61.35        66.77        81.63        95.70        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        21.37        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
      102.58        99.25       108.72       106.78        90.58        64.04 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       41.62        28.37        14.73        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65        15.62        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       73.64         5.26        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       101.95        83.87       114.02 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14       160.90        50.89        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
       84.20         2.76        76.01        53.36        85.35        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM 
       79.00        89.00        73.18       143.21        62.86        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        39.39        40.54        54.74        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
      143.38        12.13        50.70        65.72       146.50       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       68.45       234.28       172.96       162.05       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       131.21        97.48       188.68        79.63        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       73.51       139.17        68.12       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        28.50        46.95        40.83        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       56.98        51.68        32.02        25.71        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       45.57        49.94        11.67        41.75        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       48.23        17.26         3.22        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        4.41         9.63        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       24.43        37.78        35.51        23.08        41.00        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX 
       20.38         5.85         2.50        13.61        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F 
       50.79        23.93        24.95        42.35        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        2.01         7.23        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       51.16        69.93        82.85        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ 
       31.53        97.48        24.66        33.17        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       55.00        72.07       144.59        72.07        28.14        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
      109.28         8.94        18.64         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P 
       21.76         9.44        11.93        11.77        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66         0.39         2.24         1.87         1.12         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.08        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        0.43         8.28         9.53         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       11.90        20.88        13.25        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        18.90        12.03        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 
       20.09        19.40        20.38        12.20        13.32        18.58 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        21.83        17.69        15.55        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.31         6.35        15.16        15.52        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.45        13.05         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       34.26        32.02        31.96        18.51        25.41        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15G 
       21.04        23.87        23.34        22.82        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       13.02        19.56        17.06        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       33.01        32.35        16.47        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       33.73        33.70        28.44        22.65         3.88        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       43.04         5.52        15.72         8.28        30.61        26.56 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       12.85        34.82        32.88        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       39.55        12.59        35.24        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE 
       28.27         6.12         3.02        21.21         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 
       13.32        39.09        41.03        12.89        20.71         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        1.94         7.13        24.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       30.18        23.84         0.79        13.81        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       39.72        18.21        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 
       22.82        29.95        29.85        40.41        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE 
       29.82        30.08         7.86        18.90        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        34.03        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DI 
      109.87        59.57       216.76        79.10        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       86.96       115.69       106.06       101.62       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       16.08        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        2.10        36.30        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DC 
       42.77        17.36        14.07        19.73         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       16.93        16.80        13.84        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       17.03         3.81        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           220.90            234.28 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            24.53             24.56 
[1] "0.0 - 220.9 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        22       25        2        1        95        69
  8P GAIN WILD-TYPE      67       56        6        2       258       176
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           2         33          9         13        8
  8P GAIN WILD-TYPE         0        117         20         50       12
                   vv
clus                STAGE TIS STAGE X
  8P GAIN MUTATED           0       5
  8P GAIN WILD-TYPE         1       8
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 22                67
  STAGE IA                25                56
  STAGE IB                 2                 6
  STAGE II                 1                 2
  STAGE IIA               95               258
  STAGE IIB               69               176
  STAGE III                2                 0
  STAGE IIIA              33               117
  STAGE IIIB               9                20
  STAGE IIIC              13                50
  STAGE IV                 8                12
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    77 160  36   9
  8P GAIN WILD-TYPE 195 456  94  31
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              77               195
  T2             160               456
  T3              36                94
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED   135 100  26  17
  8P GAIN WILD-TYPE 366 250  91  58
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             135               366
  N1             100               250
  N2              26                91
  N3              17                58
[1] 4 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   236   8
  8P GAIN WILD-TYPE 643  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    236    8
  8P GAIN WILD-TYPE  643   13
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             236               643
  1               8                13
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   281   4
  8P GAIN WILD-TYPE 770   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    281    4
  8P GAIN WILD-TYPE  770    7
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE             281               770
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P GAIN MUTATED                            0                           219
  8P GAIN WILD-TYPE                          1                           544
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P GAIN MUTATED                               36                   3
  8P GAIN WILD-TYPE                            156                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P GAIN MUTATED                       1                                9
  8P GAIN WILD-TYPE                     3                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8P GAIN MUTATED                    3             14
  8P GAIN WILD-TYPE                 14             34
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                219               544
  INFILTRATING LOBULAR CARCINOMA                36               156
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                14                34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    79 206
  8P GAIN WILD-TYPE 209 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     79  206
  8P GAIN WILD-TYPE  209  568
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               79               209
  YES             206               568
[1] 2 2
[1] FALSE
D15V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    13
  8P GAIN WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          58   188
  8P GAIN WILD-TYPE                       112   548
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     58               112
  WHITE                                        188               548
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9 225
  8P GAIN WILD-TYPE  29 633
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  225
  8P GAIN WILD-TYPE   29  633
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                29
  NOT HISPANIC OR LATINO             225               633
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   446  64
  8Q GAIN WILD-TYPE 470  64
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              510               534 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               64                64 
$`8Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
      129.14       131.67         9.96        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04N 
       14.27        13.68        31.79        39.32        19.20       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP 
       78.41       121.94        36.13        99.12        24.79        92.48 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       75.25        98.99        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX 
       61.58        25.22        80.28        79.76        34.29        24.72 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 
       63.29        27.12        44.88        50.43        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE 
        8.38        49.84        17.46        18.90        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       21.90        21.67        18.61        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A259 
       17.36        60.72        20.25        19.20        19.56        52.47 
TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
       42.44        18.15       105.34        39.65        33.93        29.98 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       47.31        34.98        38.37        24.39        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       21.90        38.30        30.61        35.67        29.79        31.73 
TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       25.15        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE 
       22.32        10.29        11.97        14.93        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       12.10        10.72        10.29        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        17.98        53.06        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07O 
       53.98         9.01        43.00        18.97        14.01         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A086 
       10.98         8.98        24.99         9.99        18.05        13.02 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P 
       28.96        33.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 
        0.99        33.01       112.08        43.00        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K 
       17.95         9.99        12.00         1.02        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W 
       33.07         1.02        25.02         8.98        19.04         0.99 
TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E 
       14.01        19.04         0.99        27.02        17.03         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH 
       10.85         5.72        38.53        99.35        26.04        33.04 
TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6NO 
        2.27        23.24        11.44        13.71        13.58         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A049 TCGA-AN-A04C 
        0.03        20.19         0.33         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        1.71         9.96         0.16         0.33         7.00         7.59 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XS TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V 
        0.33         0.33        81.63        68.75        47.87        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A128 
       21.40        52.18        26.04        20.32        50.24       106.78 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP 
      130.09        15.62        32.52         2.56        32.91       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A0U4 
       73.64        74.79        86.66        98.93        65.36        85.97 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AU 
       61.84        52.77        51.25        39.98        43.07        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       63.62        62.14        33.73       104.28        87.22        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 
       53.36        85.35        50.96        79.00        78.48        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO 
       58.92        93.83        20.25        54.21        66.15        39.39 
TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       20.38        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN 
      149.59       220.90       129.57       112.37       126.12        84.59 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RU 
      211.56       189.01        81.17        78.02       102.77       131.21 
TCGA-B6-A0RV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X7 
      157.41        18.35        21.47       113.79       186.48        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
       43.59       101.52       170.17        85.35        74.99        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        20.45        25.55        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP 
       56.94        37.22        18.21        24.85        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL 
       45.57        49.05        41.75        44.02        45.83        48.23 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       15.65         2.56        38.47        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HB 
       44.81        10.78        15.16        24.56        23.08        26.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 
       36.85        12.89        27.25        50.79         5.59        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18U 
       44.81        23.05         7.23        26.66        37.74        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        91.99       113.82        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        31.53        89.16        97.48       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 
       74.73       122.89        45.63        72.07        26.14        83.31 
TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12M 
      130.16         8.94        23.51         9.63        18.87        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM 
        3.16         2.24         1.05        11.34        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A 
        3.25         0.36         8.28         9.67         0.03        12.20 
TCGA-C8-A8HR TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JC 
       13.41        20.58        13.97        14.17        19.20        15.78 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        12.03        12.03        14.01        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.09        21.01        13.32        14.70        18.58        17.79 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS 
       18.15        15.22        14.50        19.92        16.41        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M 
       14.24        14.14        13.05        14.43        16.41        13.48 
TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14N 
       10.09        12.53        34.42        27.52        40.11        47.15 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14X 
       44.68        38.60        33.17        33.30        43.33        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A158 
       28.60        18.51        27.12        23.24        19.43        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15J TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       19.40        11.05        13.02        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1II 
       60.53        53.62        32.35        28.50        17.10        33.70 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI 
       22.19        20.98        27.42        24.59       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        8.75        16.93         8.28        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NF 
       12.85        36.82        13.48        13.12        35.77        35.24 
TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
        9.86        34.95         2.56         2.76        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
       40.24        34.65        21.27        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS 
       23.51        17.06        27.22         1.94         0.72        29.72 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UP 
       30.18        15.72        12.33        23.84        14.70        14.40 
TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ 
        8.48        18.90        28.77        22.82        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PB 
       41.13        52.96        23.11        18.48         7.86        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DC 
        6.15        13.94        19.96        25.91       109.87        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO TCGA-GM-A3XL TCGA-GM-A5PV TCGA-HN-A2NL 
       75.02        70.85        85.35        69.30        13.55         2.60 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       11.84        11.57         7.10        15.32        14.70        14.47 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        14.70        12.36 
TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I TCGA-OL-A66N 
       14.07        58.52        31.99        58.62        23.47        26.04 
TCGA-OL-A6VO TCGA-OL-A6VR TCGA-PE-A5DC TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 
       28.21        40.11        47.01        16.50        13.12        15.39 
TCGA-S3-AA12 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R6 
       15.35        17.03         3.81        11.41        52.96       107.05 

$`8Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04P 
       47.24        20.88         7.96        28.01        18.21        18.02 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       73.84        87.25        63.12       101.98        55.43       136.73 
TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        88.60       107.93        75.55         5.19       107.93 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      101.72       134.40       107.61        74.40        72.00        35.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T4 
       31.82        61.94        99.19        54.64        44.28        20.52 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       32.55        25.28        50.47        49.48        19.33        48.46 
TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC 
       22.45        16.47       107.70        17.19        10.59        20.88 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       83.01        32.75        49.48        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       23.21        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        23.61        29.56        31.36        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       11.28        13.41        14.70        13.74        17.92        14.73 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A07E 
       11.05         9.37         1.02        29.03        31.00        19.99 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A084 
       18.97        12.00        32.05         7.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08Z 
       36.95         0.99        38.01         9.99        31.00        40.01 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09V 
       41.98        12.00         9.99        50.04        45.07        15.02 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A2B8 
       12.00        13.02        21.04        38.04         0.95         1.48 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        55.43        36.99        38.79        50.70         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       19.79        24.79         1.55        17.42        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 
        8.22         1.12         1.32         2.30         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        2.96         7.36         6.51         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XO 
        5.65         7.96         7.17         6.28         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A0J2 
       80.28        61.35        66.77        95.70        58.95        32.78 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        76.77        21.37        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12H 
       71.80       102.58        99.25       108.72        90.58        28.37 
TCGA-AO-A1KO TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV 
       14.73        26.93         5.65        19.20         5.26        42.35 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       101.95        83.87       114.02 
TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR 
       75.55        48.82        76.11        43.73        43.56        17.23 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       37.81        61.28       160.90        50.89        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A250 
       78.51        84.20         2.76        76.01        83.77        89.00 
TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       73.18       143.21        62.86        52.11        38.17        40.54 
TCGA-AR-A5QM TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
       54.74        12.13        50.70        65.72       146.50       176.98 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI 
       18.77       110.14       110.93       140.88        68.45       234.28 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS 
      172.96       162.05       140.48       100.70        89.46        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
      188.68        79.63       129.57       129.70        28.27        68.94 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ 
       73.51       139.17        68.12       103.63        71.15        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       46.95        48.36        56.98        51.68        32.02        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       21.70        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.94        11.67        48.13        42.90        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV 
       38.01        22.13        13.91        17.26         3.22        67.86 
TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       47.41         4.41         9.63        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 
       31.00        24.43        30.35        37.78        35.51        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW 
       52.96        20.38         5.85         2.50        13.61        51.32 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       23.93        24.95         8.81         2.01        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 TCGA-BH-A1FD 
       69.93        82.85        17.69        25.81        24.66        33.17 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        72.07       144.59        28.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        57.83        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 
      109.28        18.64         5.26         9.70        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 
       11.93        11.77        12.66         0.39         1.87         1.12 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 
       10.42         0.30         0.23         0.43         9.53         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ 
        0.99         0.03         0.23        13.02        12.49        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       11.90        20.88        13.25        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JM 
       17.49        16.50        18.71        18.90        18.97        19.40 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       20.38        12.20        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
       12.39        17.16        14.73        21.83        17.69        15.55 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.85         6.35        15.16        17.42        16.04        13.45 
TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
        9.44         4.80         0.76        13.08        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P 
       46.59        40.41        37.51        28.44        28.87        40.96 
TCGA-E2-A14Q TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 
       38.24        34.26        32.02        25.41        21.04        23.87 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P 
       18.21        12.92        17.42         9.04        20.58        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       53.03        33.01        16.47        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 
       33.73        28.44        22.65         3.88        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       39.62        19.66        40.47        28.90        18.87        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N8 
        5.52        15.72        30.61        34.82        32.88        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       36.56        39.55        12.59        25.84        11.90        28.27 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH 
        6.12         3.02        21.21         1.12         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D 
       35.64        34.13        32.05        12.53        13.32        41.03 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
       20.71         0.69         7.13        24.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       18.41         0.79        13.81        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.21        13.25        16.57        15.68        25.94        29.95 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF 
       39.78        29.82        30.08        18.90        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        23.51         7.40        59.57       216.76        79.10 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX 
      110.50        38.20        43.73        66.38        72.03        18.12 
TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       62.43        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP 
       11.44        10.95        25.05        17.06        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        2.63        14.73        27.91        22.39         2.10        36.30 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       20.38        26.70        65.62        41.92        42.77        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       14.07        19.73         8.91        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 
        0.26         9.93        16.93        16.80        13.84        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       13.84        13.94        29.03        15.35        16.04       108.07 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           220.90            234.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           23.755            25.000 
[1] "0.0 - 220.9 (23.8)" "0.0 - 234.3 (25.0)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        45       37        3        1       182       106
  8Q GAIN WILD-TYPE      44       44        5        2       171       139
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           2         74         15         31       12
  8Q GAIN WILD-TYPE         0         76         14         32        8
                   vv
clus                STAGE TIS STAGE X
  8Q GAIN MUTATED           0       9
  8Q GAIN WILD-TYPE         1       4
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 45                44
  STAGE IA                37                44
  STAGE IB                 3                 5
  STAGE II                 1                 2
  STAGE IIA              182               171
  STAGE IIB              106               139
  STAGE III                2                 0
  STAGE IIIA              74                76
  STAGE IIIB              15                14
  STAGE IIIC              31                32
  STAGE IV                12                 8
  STAGE TIS                0                 1
  STAGE X                  9                 4
[1] 13  2
[1] TRUE
[1] "dimension of 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   137 304  56  20
  8Q GAIN WILD-TYPE 135 312  74  20
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1             137               135
  T2             304               312
  T3              56                74
  T4              20                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   247 159  63  38
  8Q GAIN WILD-TYPE 254 191  54  37
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             247               254
  N1             159               191
  N2              63                54
  N3              38                37
[1] 4 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   441  12
  8Q GAIN WILD-TYPE 438   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    441   12
  8Q GAIN WILD-TYPE  438    9
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             441               438
  1              12                 9
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   513   7
  8Q GAIN WILD-TYPE 538   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    513    7
  8Q GAIN WILD-TYPE  538    4
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             513               538
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q GAIN MUTATED                            1                           412
  8Q GAIN WILD-TYPE                          0                           351
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q GAIN MUTATED                               55                   5
  8Q GAIN WILD-TYPE                            137                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q GAIN MUTATED                       1                               13
  8Q GAIN WILD-TYPE                     3                               17
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8Q GAIN MUTATED                    4             28
  8Q GAIN WILD-TYPE                 13             20
D16V8, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                412               351
  INFILTRATING LOBULAR CARCINOMA                55               137
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)              13                17
  MUCINOUS CARCINOMA                             4                13
  OTHER  SPECIFY                                28                20
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   158 362
  8Q GAIN WILD-TYPE 130 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    158  362
  8Q GAIN WILD-TYPE  130  412
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              158               130
  YES             362               412
[1] 2 2
[1] FALSE
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1    28
  8Q GAIN WILD-TYPE                                0    32
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          98   336
  8Q GAIN WILD-TYPE                        72   400
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         28                32
  BLACK OR AFRICAN AMERICAN                     98                72
  WHITE                                        336               400
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    13 416
  8Q GAIN WILD-TYPE  25 442
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13  416
  8Q GAIN WILD-TYPE   25  442
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                25
  NOT HISPANIC OR LATINO             416               442
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED   120  19
  9P GAIN WILD-TYPE 796 109
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              139               905 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               109 
$`9P GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM 
       11.44        31.79        73.84        87.25       101.98        24.79 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM 
       75.55        98.99        50.43         8.38        49.84        31.73 
TCGA-A2-A1FV TCGA-A2-A25D TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 
       23.47        18.15        21.14        33.11        20.19        10.29 
TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A07F TCGA-A8-A07R 
       14.70        14.50        14.73        10.42        18.97         8.98 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08X TCGA-A8-A093 
       24.99        45.07        38.01        28.96        43.00        17.95 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A3W5 
       14.01         2.37         5.72        38.53        26.04        16.57 
TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV 
       13.71         1.12         0.33         7.00         7.04         0.33 
TCGA-AN-A0FX TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JL TCGA-AO-A128 TCGA-AQ-A54N 
        0.33        20.32        53.03        55.33       106.78         2.56 
TCGA-AR-A0U0 TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-B6-A0I2 
       65.36        33.73       160.90        89.00        93.83       143.38 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU 
      112.37       176.98       140.88       211.56       100.70       131.21 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0B9 
      129.57       186.48        43.59        73.51        25.55        51.68 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0RX 
       37.22        24.85        45.57        32.58        31.00         5.59 
TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 
        8.81        55.63        51.16        42.28        12.00        25.81 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A132 
       97.48       114.15        26.14        18.64         5.26         1.87 
TCGA-C8-A138 TCGA-C8-A26Z TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 
        4.08         8.28        13.02        20.58        21.14        14.17 
TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF 
       16.50        18.15        18.90        13.32        18.15        15.22 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27V TCGA-D8-A3Z6 
       14.50        19.92        12.99        12.66        12.53        18.51 
TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       37.51        47.15        19.43        14.79        25.05        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 
       17.10        33.73        33.70        19.66        43.04        16.93 
TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY 
        8.28        12.85        13.48         0.69        26.07         8.48 
TCGA-EW-A1J1 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GM-A2DF 
       18.90         7.86         6.15        34.55        19.96        70.85 
TCGA-GM-A2DH TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-LL-A5YM TCGA-LL-A6FR TCGA-MS-A51U 
       72.10        69.30        72.03        15.32        16.08        22.39 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF 
       36.36        23.47        28.21        86.96         9.93        16.50 
TCGA-S3-AA0Z 
       16.80 

$`9P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        55.43        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       92.48        88.60       107.93        75.25         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.52        17.13        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       49.48        18.61        19.33        48.46        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        42.44        17.19       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        21.30        23.21        26.96        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.31        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        31.73        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       11.34        10.59        11.28        13.41        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        21.17        17.92        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        32.05         9.99        10.98         7.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        33.01       112.08        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM 
       17.03        38.04         0.95        10.85         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       14.99        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        0.03        20.19         1.32         2.30         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.28 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       52.18        26.04        37.48        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       62.04        71.80       102.58        99.25       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       61.28        63.62        62.14        50.89        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        73.18        72.76        58.92       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        74.99        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        59.84        20.45        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BC 
       39.55        39.16        48.36        56.94        56.98        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        46.19        24.49        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       36.85        12.89        51.32        27.25        50.79        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 
      113.82        82.85        55.69        49.58        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       11.93        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        2.24         1.12         1.05         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 
        3.25         0.30         0.23         0.36         0.43         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.53         0.03         9.50        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
        0.23        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        13.97        14.17        13.48        19.20        17.49 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        15.78        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58        12.39        17.16        14.73        21.83 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        15.55        16.41        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.26        33.37        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.10        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        28.60        18.51        25.41        27.12        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       16.47        38.30        37.41        32.78        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       39.62        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      102.61         8.75         5.52        15.72        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       26.56        34.29        34.82        32.88        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02         2.76        21.21        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       22.75        41.03        12.89        23.51        20.71        17.06 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         7.13        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.79        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       39.72        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR 
       18.90        19.99        13.94        10.52        14.43        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       23.51         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        75.02        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.43        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       11.44        10.95        25.05        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.79        22.26         2.63        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       14.70        12.36        14.73        14.07        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       28.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       41.92        42.77        26.04        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21         0.16         0.26 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       13.12        16.93        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.33              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           211.56            234.28 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.39             24.59 
[1] "0.3 - 211.6 (22.4)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1"  
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         9        6        1        1        56        34
  9P GAIN WILD-TYPE      80       75        7        2       297       211
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0         11          4         12        3
  9P GAIN WILD-TYPE         2        139         25         51       17
                   vv
clus                STAGE TIS STAGE X
  9P GAIN MUTATED           0       1
  9P GAIN WILD-TYPE         1      12
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 6                75
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA               56               297
  STAGE IIB               34               211
  STAGE III                0                 2
  STAGE IIIA              11               139
  STAGE IIIB               4                25
  STAGE IIIC              12                51
  STAGE IV                 3                17
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    28  90  14   8
  9P GAIN WILD-TYPE 244 526 116  32
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              28               244
  T2              90               526
  T3              14               116
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    66  47  11  14
  9P GAIN WILD-TYPE 435 303 106  61
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              66               435
  N1              47               303
  N2              11               106
  N3              14                61
[1] 4 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   117   3
  9P GAIN WILD-TYPE 762  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    117    3
  9P GAIN WILD-TYPE  762   18
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0             117               762
  1               3                18
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED   141   0
  9P GAIN WILD-TYPE 910  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    141    0
  9P GAIN WILD-TYPE  910   11
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE             141               910
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P GAIN MUTATED                            0                           110
  9P GAIN WILD-TYPE                          1                           653
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P GAIN MUTATED                               20                   2
  9P GAIN WILD-TYPE                            172                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P GAIN MUTATED                       2                                1
  9P GAIN WILD-TYPE                     2                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9P GAIN MUTATED                    1              5
  9P GAIN WILD-TYPE                 16             43
D17V8, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                110               653
  INFILTRATING LOBULAR CARCINOMA                20               172
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 5                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    37 104
  9P GAIN WILD-TYPE 251 670
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37  104
  9P GAIN WILD-TYPE  251  670
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               37               251
  YES             104               670
[1] 2 2
[1] FALSE
D17V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     8
  9P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          30    94
  9P GAIN WILD-TYPE                       140   642
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     30               140
  WHITE                                         94               642
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5 115
  9P GAIN WILD-TYPE  33 743
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5  115
  9P GAIN WILD-TYPE   33  743
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                33
  NOT HISPANIC OR LATINO             115               743
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    98  18
  9Q GAIN WILD-TYPE 818 110
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              116               928 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18               110 
$`9Q GAIN MUTATED`
TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS 
       42.81        11.44        31.79        73.84        87.25        75.55 
TCGA-A2-A0CV TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25B 
       98.99         8.38        49.84        31.73        23.47        42.44 
TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A6VX 
       21.14        33.11        20.19        10.29        14.70        10.42 
TCGA-A8-A07F TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A09X 
       18.97        45.07        38.01        28.96        17.95        14.01 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2FM TCGA-AN-A04A TCGA-AN-A0FK TCGA-AN-A0FT 
        2.37         5.72        26.04         2.96         7.00         7.04 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AQ-A04H 
        0.33         0.33         0.33        20.32       106.78        24.79 
TCGA-AR-A0TR TCGA-AR-A1AJ TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A5QM 
        5.26        52.77       160.90        89.00        93.83        54.74 
TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RS 
      143.38       112.37       176.98        18.77       140.88       100.70 
TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0BA TCGA-BH-A0BG 
      131.21       129.57        73.51        25.55        37.22        24.85 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A18F TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV 
       46.19        32.58         8.81        51.16        42.28        12.00 
TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A12M 
       31.53       114.15        26.14        18.64         5.26        11.77 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A275 
        1.87         4.08        11.34        12.03         0.43         0.03 
TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JE 
       13.02        20.58        21.14        14.17        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XU 
       12.03        13.32        18.15        15.22        19.92        12.99 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A1BD 
       12.53        18.51        37.51        47.15        19.43        17.10 
TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A9RU 
       33.70        19.66        43.04        16.93         8.28        12.85 
TCGA-E9-A1N6 TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 
       13.48        12.89         0.69        26.07         8.48        18.90 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GI-A2C8 
       29.82         7.86         6.15        34.55        19.96         7.40 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I TCGA-PE-A5DE 
       70.85        69.30        22.39        36.36        23.47        86.96 
TCGA-S3-AA0Z TCGA-Z7-A8R6 
       16.80       107.05 

$`9Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       104.81        18.02        78.41       121.94        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        17.13        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.77        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
      105.34        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        49.48        47.31        34.98        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.90        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       37.45        35.67        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04         0.95        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55        11.44        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        5.65         7.96         7.59         7.17         6.28         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       102.58        99.25       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        32.91        19.20       111.32        73.64        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       61.84        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        33.73        50.89        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        73.18        72.76        58.92       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        20.38        16.04        20.45        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE 
      146.50       126.12        84.59       110.14       110.93       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       102.77       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.63        18.35        21.47       113.79       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        85.35        74.99        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        24.53        59.84        20.45        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       51.68        32.02        18.21        25.71        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE 
       15.68        14.30         9.63        44.81        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       82.85        55.69        49.58        17.69        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
        1.12         1.05         4.11        12.33        10.92        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A 
        0.36         8.28         9.67         9.53         9.50        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.99         0.03         0.23        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       11.90        20.88        13.25        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF 
       19.20        17.49        16.50        18.71        15.78        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.83        14.50        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31         6.35        15.16        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.48         4.80         0.76        10.09        13.08        12.26 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       18.51        25.41        27.12        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        16.47        38.30        37.41        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        39.62        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       106.75       102.61         8.75         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        26.56        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        32.09        40.24         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        41.03        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
       29.72         0.76        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       12.20        39.72        18.21        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR 
       18.90        19.99        13.94        10.52        14.43        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       23.51       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       15.68         7.46        14.50        14.70        12.36        14.73 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.07        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       47.01        64.21         0.16         0.26         9.93        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       13.12        16.93        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       29.03        15.35        16.04       108.07 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           176.98            234.28 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           20.255            24.790 
[1] "0.0 - 177.0 (20.3)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         8        4        1        1        46        31
  9Q GAIN WILD-TYPE      81       77        7        2       307       214
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           0         12          5          7        2
  9Q GAIN WILD-TYPE         2        138         24         56       18
                   vv
clus                STAGE TIS STAGE X
  9Q GAIN MUTATED           0       0
  9Q GAIN WILD-TYPE         1      13
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  8                81
  STAGE IA                 4                77
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA               46               307
  STAGE IIB               31               214
  STAGE III                0                 2
  STAGE IIIA              12               138
  STAGE IIIB               5                24
  STAGE IIIC               7                56
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    23  77  12   6
  9Q GAIN WILD-TYPE 249 539 118  34
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              23               249
  T2              77               539
  T3              12               118
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    55  44   9   9
  9Q GAIN WILD-TYPE 446 306 108  66
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              55               446
  N1              44               306
  N2               9               108
  N3               9                66
[1] 4 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   101   2
  9Q GAIN WILD-TYPE 778  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    101    2
  9Q GAIN WILD-TYPE  778   19
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0             101               778
  1               2                19
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED   118   0
  9Q GAIN WILD-TYPE 933  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    118    0
  9Q GAIN WILD-TYPE  933   11
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE             118               933
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q GAIN MUTATED                            0                            89
  9Q GAIN WILD-TYPE                          1                           674
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q GAIN MUTATED                               18                   3
  9Q GAIN WILD-TYPE                            174                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q GAIN MUTATED                       2                                1
  9Q GAIN WILD-TYPE                     2                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9Q GAIN MUTATED                    1              4
  9Q GAIN WILD-TYPE                 16             44
D18V8, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 89               674
  INFILTRATING LOBULAR CARCINOMA                18               174
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 4                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    33  85
  9Q GAIN WILD-TYPE 255 689
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     33   85
  9Q GAIN WILD-TYPE  255  689
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               33               255
  YES              85               689
[1] 2 2
[1] FALSE
D18V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0    11
  9Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          18    83
  9Q GAIN WILD-TYPE                       152   653
D18V11, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     18               152
  WHITE                                         83               653
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4 100
  9Q GAIN WILD-TYPE  34 758
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4  100
  9Q GAIN WILD-TYPE   34  758
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO             100               758
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED   181  29
  10P GAIN WILD-TYPE 735  99
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               210                834 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                 99 
$`10P GAIN MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U 
       43.43        48.10        28.01        18.02        78.41        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.79        33.76        79.76        31.82        44.88        50.43 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YJ 
       17.13         8.38        49.84        20.75        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A7-A0DA 
       31.73        19.20        42.44        33.93        83.01        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       31.73        20.19        23.74        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X 
       17.92        14.73        10.29        13.02         1.02        31.00 
TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B 
       17.03        43.00         8.98        24.99        45.07        38.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        43.00        30.97         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK 
       50.04        49.05        25.02        14.01         2.37        38.53 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS 
       11.44        13.71         1.12         1.78         1.71         0.33 
TCGA-AN-A0FZ TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 
        0.33        81.63        29.13        32.78        21.40        53.03 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A1KR TCGA-AO-A1KS 
       55.33       102.58       106.78        90.58        70.39         0.53 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TT 
      130.09         2.56        32.91        19.20        74.79        86.66 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AW 
       85.97        61.84        52.77        51.25        43.07        63.62 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V 
       33.73       160.90        50.89        97.84        53.36        85.35 
TCGA-AR-A251 TCGA-AR-A2LL TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       78.48        66.15       129.57        65.72       112.37       176.98 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0X1 
       84.59       110.14       140.88       211.56       162.05       186.48 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B6 
       43.59       101.52        74.99        20.45        25.55        56.94 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 
       24.85        44.05        41.75         2.56        38.47         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HU 
       44.81        32.58        31.00        30.35        23.08        12.89 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EV 
       50.79         5.59        26.66         7.36        69.93        12.00 
TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-C8-A12O TCGA-C8-A12P 
       55.69        31.53        97.48       114.15        12.66        11.77 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A274 
       12.66         3.16         2.24         2.30         0.36         9.53 
TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB 
        0.99        13.02        20.88        13.97        19.20        18.71 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XF 
       18.15        12.03        20.09        18.58        23.90        15.22 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A14N 
       12.99        12.66        15.32        18.51        34.42        47.15 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 
       44.68        38.60        25.41        27.12        19.43        25.05 
TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 
       18.21        60.53       106.75       102.61         8.75        16.93 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH 
       34.92        26.56        13.48        13.12        32.09        34.59 
TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5UP 
       41.03         0.69        27.22         0.72        30.18        14.40 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PB TCGA-EW-A1PC 
       28.77        25.94        22.82        40.41        19.99         6.15 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DB 
       19.96        52.73        25.91        10.16       109.87        79.10 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YM 
       70.85        72.10        11.84         7.10        10.62        15.32 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5S0 
       14.47         2.63         7.46        14.73        22.39        20.38 
TCGA-OL-A6VO TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       28.21        16.80        15.39        13.94        17.03         3.81 

$`10P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH 
       48.36         9.96         8.52        14.37        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
       18.21       104.81       121.94        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40        80.28       107.61        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       35.05        34.29        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 
       54.64        27.12        44.28        17.52        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F 
       35.47        30.61        37.45        33.11        29.79        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J 
       23.61        29.56        31.36        24.26        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        11.97        13.74        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R 
       11.05         9.37        10.42         8.75        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 
        9.99        10.98         7.99         9.99        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       36.95        13.02         0.99        28.96        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
        9.99        31.00         0.99        33.01       112.08        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       33.01        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
        1.02        45.07        29.98        33.07         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         5.72         1.48        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y 
       16.57        19.79        23.24        24.79         1.55        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       20.19         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.62         2.96         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        61.35        66.77        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       47.87        58.95        52.18        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        50.24        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.72       108.03        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       41.62        28.37        14.73        82.62        61.87        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93         5.65        15.62        32.52       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       73.64         5.26        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH 
      107.24        65.36       101.95        83.87       114.02        75.55 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       48.82        76.11        43.73        43.56        39.98        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M 
       37.81        76.21        61.28        62.14        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         2.76       104.28        87.22        76.01 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        79.00        89.00        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       143.21        20.25        62.86        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
       12.13       220.90        50.70       146.50        18.77       126.12 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        24.53        59.84        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        48.36        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       17.26        15.65         3.22        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI 
        4.41        15.68        14.30        46.19        24.49        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        51.32        27.25        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 
       42.28        49.58        17.69        25.81        89.16        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         0.39         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.43         8.28         9.67         0.03         9.50        12.20 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.03         0.23        12.49        13.41        19.46        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       13.25        20.58        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        16.50        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.12        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        17.79        16.73        25.74 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15        12.39        17.16        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        15.55        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31         6.35        15.16        16.54        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 
       10.09        13.08        12.53        12.26        33.37        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       16.18         8.02        12.10        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P 
       40.41        37.51        40.11        28.44        28.87        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       31.96        28.60        18.51        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       18.87        43.04         5.52        15.72         8.28        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       34.29        12.85        34.82        32.88        36.82        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02         2.76        21.21        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        21.27        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
       20.71        17.06         1.94         7.13        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        26.07        18.41        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70         0.79        13.81        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.95        29.85        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD 
       23.11        18.48        30.08         7.86        18.90        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        14.43        34.55        55.00        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       17.49        23.51         7.40        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       75.02        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX 
       72.03        13.55        18.12         2.60        62.43        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       21.24        13.22        13.28        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       25.05        17.06        14.70        14.79        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68        14.50        14.70        12.36        14.07        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G 
       16.93        13.84        15.35        14.96        13.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.33               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            211.56             234.28 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             26.61              23.69 
[1] "0.3 - 211.6 (26.6)" "0.0 - 234.3 (23.7)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED        17       12        1        0        79        40
  10P GAIN WILD-TYPE      72       69        7        3       274       205
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           0         28          7         13        8
  10P GAIN WILD-TYPE         2        122         22         50       12
                    vv
clus                 STAGE TIS STAGE X
  10P GAIN MUTATED           1       3
  10P GAIN WILD-TYPE         0      10
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                 12                 69
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                79                274
  STAGE IIB                40                205
  STAGE III                 0                  2
  STAGE IIIA               28                122
  STAGE IIIB                7                 22
  STAGE IIIC               13                 50
  STAGE IV                  8                 12
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    45 130  23  12
  10P GAIN WILD-TYPE 227 486 107  28
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               45                227
  T2              130                486
  T3               23                107
  T4               12                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED   106  57  27  17
  10P GAIN WILD-TYPE 395 293  90  58
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0              106                395
  N1               57                293
  N2               27                 90
  N3               17                 58
[1] 4 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   179   8
  10P GAIN WILD-TYPE 700  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    179    8
  10P GAIN WILD-TYPE  700   13
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0              179                700
  1                8                 13
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   210   2
  10P GAIN WILD-TYPE 841   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    210    2
  10P GAIN WILD-TYPE  841    9
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE              210                841
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P GAIN MUTATED                            0                           181
  10P GAIN WILD-TYPE                          1                           582
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P GAIN MUTATED                               16                   4
  10P GAIN WILD-TYPE                            176                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P GAIN MUTATED                       1                                4
  10P GAIN WILD-TYPE                     3                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10P GAIN MUTATED                    0              6
  10P GAIN WILD-TYPE                 17             42
D19V8, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 181                582
  INFILTRATING LOBULAR CARCINOMA                 16                176
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  6                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    68 144
  10P GAIN WILD-TYPE 220 630
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     68  144
  10P GAIN WILD-TYPE  220  630
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                68                220
  YES              144                630
[1] 2 2
[1] FALSE
D19V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1    11
  10P GAIN WILD-TYPE                                0    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          51   129
  10P GAIN WILD-TYPE                       119   607
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          11                 49
  BLACK OR AFRICAN AMERICAN                      51                119
  WHITE                                         129                607
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7 166
  10P GAIN WILD-TYPE  31 692
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7  166
  10P GAIN WILD-TYPE   31  692
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 31
  NOT HISPANIC OR LATINO              166                692
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED   103  18
  10Q GAIN WILD-TYPE 813 110
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               121                923 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                18                110 
$`10Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A0CM 
       48.10        28.01        18.02        78.41        87.25        24.79 
TCGA-A2-A0EQ TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A3XS TCGA-A7-A13E 
       79.76        50.43        17.13        20.75        33.93        20.19 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07Z 
       23.74        21.73        13.02        31.00        17.03        45.07 
TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09Q 
       38.01        31.00        30.97         9.99        50.04        25.02 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A62V TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0FZ 
       14.01         2.37        11.44        13.71         1.78         0.33 
TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 TCGA-AO-A128 TCGA-AO-A12A 
       81.63        32.78        21.40        53.03       106.78        90.58 
TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI 
        0.53       130.09         2.56        74.79        86.66        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S 
       52.77        43.07        63.62       160.90        50.89        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       53.36        85.35       129.57        65.72       112.37       176.98 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A1KC TCGA-BH-A0AY 
      110.14       140.88       162.05        79.63        43.59        25.55 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 
       56.94        44.05         2.56        38.47         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV TCGA-C8-A12O 
       32.58        31.00        26.66        69.93        12.00        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A274 TCGA-C8-A8HP 
       11.77        12.66         3.16         2.30         9.53        13.02 
TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1X9 
       20.88        19.20        18.71        18.15        12.03        23.90 
TCGA-D8-A1XL TCGA-D8-A1XZ TCGA-E2-A107 TCGA-E2-A14O TCGA-E2-A150 TCGA-E2-A152 
       19.92        15.32        34.42        44.68        25.41        27.12 
TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1LI TCGA-E2-A2P5 
       19.43        18.21        14.07        60.53       102.61        16.93 
TCGA-E2-A573 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22D 
       34.92        13.48        13.12        32.09        34.59        41.03 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV 
       27.22         0.72        30.18        14.40        28.77        25.94 
TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LD-A9QF TCGA-LL-A5YM 
        6.15        10.16        79.10        72.10        10.62        15.32 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-MS-A51U TCGA-OL-A5S0 TCGA-S3-AA0Z 
       14.47         2.63         7.46        22.39        20.38        16.80 
TCGA-S3-AA10 
       15.39 

$`10Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        43.43        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
       19.20        18.21       104.81       121.94        73.84        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
      101.98        55.43        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       98.99       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       18.90        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       35.47        30.61        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        17.98        53.06        29.03        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        28.96        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       43.00        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00         1.02        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70        33.04         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79         1.55        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        5.33         5.59        80.28        61.35        66.77        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 
       68.75        47.87        58.95        29.13        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       102.58        99.25       108.72       108.03 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93         5.65        15.62        32.52        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        73.64         5.26        42.35        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86       107.24        65.36       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       85.97        75.55        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        17.23        37.81        76.21        61.28 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       62.14        33.73        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X 
        2.76       104.28        87.22        76.01        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        89.00        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
       12.13       220.90        50.70       146.50        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.93       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       89.46       131.21       157.41        97.48       188.68        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88       101.52        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        74.99        68.12       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        20.45        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        48.36        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        24.85        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       48.23        17.26        15.65         3.22        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB 
       16.27         4.41        15.68        14.30        46.19        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28         8.94        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         0.39         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
        0.36         0.43         8.28         9.67         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
       12.20         0.99         0.03         0.23        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        11.90        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.48        21.14        14.17        17.49        16.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA 
       14.70        18.58        17.79        16.73        25.74        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
        6.35        12.99        15.16        12.66        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        0.76        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       18.51        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04         5.52        15.72         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       26.56        34.29        12.85        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        6.12         3.02         2.76        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
        1.12        34.65         6.58        21.27        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
       32.05        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       23.51        20.71        17.06         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56        29.72         0.76        26.07        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       12.33        23.84        14.70         0.79        13.81        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       22.09        34.03        17.49        23.51         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       216.76        83.34        75.02        70.85        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       13.22         7.10        13.28        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       25.05        17.06        14.70        14.79        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68        14.50        14.70        12.36        14.73        14.07 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.50        13.12        16.93        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.33               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            176.98             234.28 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             26.66              23.93 
[1] "0.3 - 177.0 (26.7)" "0.0 - 234.3 (23.9)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         9        8        0        0        44        28
  10Q GAIN WILD-TYPE      80       73        8        3       309       217
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           0         17          5          5        3
  10Q GAIN WILD-TYPE         2        133         24         58       17
                    vv
clus                 STAGE TIS STAGE X
  10Q GAIN MUTATED           1       1
  10Q GAIN WILD-TYPE         0      12
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  8                 73
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                44                309
  STAGE IIB                28                217
  STAGE III                 0                  2
  STAGE IIIA               17                133
  STAGE IIIB                5                 24
  STAGE IIIC                5                 58
  STAGE IV                  3                 17
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    24  80  13   5
  10Q GAIN WILD-TYPE 248 536 117  35
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               24                248
  T2               80                536
  T3               13                117
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    62  37  14   6
  10Q GAIN WILD-TYPE 439 313 103  69
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               62                439
  N1               37                313
  N2               14                103
  N3                6                 69
[1] 4 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   108   3
  10Q GAIN WILD-TYPE 771  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    108    3
  10Q GAIN WILD-TYPE  771   18
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0              108                771
  1                3                 18
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   122   1
  10Q GAIN WILD-TYPE 929  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    122    1
  10Q GAIN WILD-TYPE  929   10
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE              122                929
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q GAIN MUTATED                            0                           103
  10Q GAIN WILD-TYPE                          1                           660
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q GAIN MUTATED                               10                   3
  10Q GAIN WILD-TYPE                            182                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q GAIN MUTATED                       1                                3
  10Q GAIN WILD-TYPE                     3                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10Q GAIN MUTATED                    0              3
  10Q GAIN WILD-TYPE                 17             45
D20V8, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 103                660
  INFILTRATING LOBULAR CARCINOMA                 10                182
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  3                 45
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    42  81
  10Q GAIN WILD-TYPE 246 693
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     42   81
  10Q GAIN WILD-TYPE  246  693
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                42                246
  YES               81                693
[1] 2 2
[1] FALSE
D20V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     8
  10Q GAIN WILD-TYPE                                0    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                          24    79
  10Q GAIN WILD-TYPE                       146   657
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      24                146
  WHITE                                          79                657
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  95
  10Q GAIN WILD-TYPE  33 763
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   95
  10Q GAIN WILD-TYPE   33  763
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 33
  NOT HISPANIC OR LATINO               95                763
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED   118  17
  11P GAIN WILD-TYPE 798 111
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               135                909 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                111 
$`11P GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04U TCGA-A2-A04W 
      129.14        20.88        31.79         7.96        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU 
       55.43        24.79        75.25        67.33        80.28        34.29 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1G1 
        8.38        49.84        20.75        18.21        17.36        19.20 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A26F 
       39.65        83.01        38.30        30.61        29.79        24.26 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD 
       23.74        20.61        10.59        10.29        14.70        14.50 
TCGA-A7-A6VX TCGA-A8-A075 TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I 
       10.42        17.03        18.97         8.98        38.01        12.00 
TCGA-A8-A091 TCGA-A8-A09A TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A6 
       33.01         9.99        29.98        33.07        25.02        21.04 
TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C 
        0.99         0.95         5.72        11.44        17.42         1.78 
TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XU 
        9.96         0.33         7.00         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A0J3 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AQ-A04L 
       80.28        21.40       108.72        90.58        98.27       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TW TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A250 TCGA-AR-A2LR 
       15.62        98.93        50.89        85.35        89.00        20.38 
TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0RS TCGA-B6-A0X0 TCGA-B6-A1KI 
      143.38       129.57       112.37       100.70       129.70        73.51 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0DG 
       68.12        24.53        24.85        21.70        45.57        23.44 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18V 
       17.26        15.65        24.43        30.35        72.56        51.16 
TCGA-BH-A1EO TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A27A 
       91.99        26.14        57.83       130.16        12.66        12.20 
TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XY TCGA-D8-A1Y0 
       13.25        12.03        15.22        14.50        16.54        15.52 
TCGA-D8-A1Y3 TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15M 
       14.14        44.68        34.26        27.12        23.34        11.05 
TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BC TCGA-E2-A1II TCGA-E2-A1IU TCGA-E2-A574 
       17.06        60.53        16.47        33.70        11.08        26.56 
TCGA-E9-A1N8 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A243 
       12.00         6.12         2.76        32.09        34.65        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1J6 
        0.69        27.22         7.13         0.79        18.90        28.77 
TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2DB 
       29.85        23.11        19.99        17.49        10.16        79.10 
TCGA-GM-A2DH TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A73Y TCGA-OL-A66I TCGA-OL-A6VO 
       72.10         2.60        11.44        15.68        23.47        28.21 
TCGA-PL-A8LZ TCGA-S3-AA17 TCGA-UU-A93S 
        9.93        13.94         3.81 

$`11P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        13.68        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
      104.81        18.02        78.41       121.94        73.84        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        99.12       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55         5.19        98.99       107.93        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72       134.40 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      107.61        79.76        74.40        72.00        35.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 
       44.88        50.43        44.28        17.52        17.13        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        23.47        60.72        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
      105.34        10.59        20.88        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF 
       23.80        21.73        22.32        11.34        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99        24.99         9.99        45.07        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       15.06        36.95        13.02         0.99        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       33.01       112.08        43.00        40.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       49.05        45.07         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 
        0.99        14.01        12.00        19.04        13.02        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         2.37        10.85         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79         1.55        13.71        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         1.71         7.36         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.33         5.59        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       68.75        47.87        58.95        29.13        32.78        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      106.78       108.03        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       17.79        24.79        26.93         5.65        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       86.66        42.35        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      101.95        83.87       114.02        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        33.73       160.90        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       76.01        53.36        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59        12.13       220.90        50.70        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       172.96       162.05       102.77       140.48        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       129.57       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       58.88        43.59       101.52       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       74.99       103.63        71.15        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       25.71        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.69        53.95        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       44.02        48.13        42.90        45.83        31.17        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       22.13        13.91        48.23         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        69.93       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O 
      144.59        72.07        28.14        38.60        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q 
        9.44        11.93        11.77        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        2.24         1.87         1.12         1.05         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        0.99         0.03         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        11.90        20.88        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       12.66        15.32         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        18.51        25.41        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        25.05        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        13.02        19.56        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       53.03        33.01        32.35        28.50        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.73        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        20.98        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        13.48        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
       34.95         2.56         3.02        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
       12.89        23.51        20.71         1.94        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        23.84        14.70        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        22.82        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        29.82        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       23.51         7.40       109.87        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       24.95        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z 
       14.47        14.79        22.26         2.63        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        14.07        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG 
       64.21        86.96         0.16         0.26        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       13.84        17.03        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.33               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            143.38             234.28 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             23.11              24.79 
[1] "0.3 - 143.4 (23.1)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED        10       13        2        1        52        27
  11P GAIN WILD-TYPE      79       68        6        2       301       218
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         15          3          6        4
  11P GAIN WILD-TYPE         2        135         26         57       16
                    vv
clus                 STAGE TIS STAGE X
  11P GAIN MUTATED           0       2
  11P GAIN WILD-TYPE         1      11
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 13                 68
  STAGE IB                  2                  6
  STAGE II                  1                  2
  STAGE IIA                52                301
  STAGE IIB                27                218
  STAGE III                 0                  2
  STAGE IIIA               15                135
  STAGE IIIB                3                 26
  STAGE IIIC                6                 57
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    33  82  15   4
  11P GAIN WILD-TYPE 239 534 115  36
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               33                239
  T2               82                534
  T3               15                115
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    73  40  10   9
  11P GAIN WILD-TYPE 428 310 107  66
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               73                428
  N1               40                310
  N2               10                107
  N3                9                 66
[1] 4 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   113   4
  11P GAIN WILD-TYPE 766  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    113    4
  11P GAIN WILD-TYPE  766   17
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0              113                766
  1                4                 17
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED   133   2
  11P GAIN WILD-TYPE 918   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    133    2
  11P GAIN WILD-TYPE  918    9
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE              133                918
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P GAIN MUTATED                            0                           111
  11P GAIN WILD-TYPE                          1                           652
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P GAIN MUTATED                               10                   1
  11P GAIN WILD-TYPE                            182                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P GAIN MUTATED                       1                                1
  11P GAIN WILD-TYPE                     3                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11P GAIN MUTATED                    2              9
  11P GAIN WILD-TYPE                 15             39
D21V8, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 111                652
  INFILTRATING LOBULAR CARCINOMA                 10                182
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  9                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    39  96
  11P GAIN WILD-TYPE 249 678
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     39   96
  11P GAIN WILD-TYPE  249  678
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                39                249
  YES               96                678
[1] 2 2
[1] FALSE
D21V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     5
  11P GAIN WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                          20    96
  11P GAIN WILD-TYPE                       150   640
D21V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      20                150
  WHITE                                          96                640
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6 109
  11P GAIN WILD-TYPE  32 749
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6  109
  11P GAIN WILD-TYPE   32  749
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO              109                749
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    75  17
  11Q GAIN WILD-TYPE 841 111
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                92                952 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                111 
$`11Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0EY 
       20.88        31.79        67.33        80.28        34.29        63.29 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A26F 
       18.21        18.61        19.20        83.01        38.30        24.26 
TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A6VX TCGA-A8-A075 TCGA-A8-A07F 
       23.74        10.59        10.29        10.42        17.03        18.97 
TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A09A TCGA-A8-A09Q 
       18.97         8.98        38.01        12.00         9.99        25.02 
TCGA-A8-A0A7 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0FK 
        0.99        11.44        17.42         1.78         9.96         7.00 
TCGA-AN-A0FY TCGA-AN-A0XU TCGA-AO-A12A TCGA-AO-A12B TCGA-AQ-A04L TCGA-AR-A0TW 
        0.33         0.33        90.58        98.27       130.09        98.93 
TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0X0 
       50.89        85.35        65.72       110.14       100.70       129.70 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0DG 
       73.51        68.12        24.85        21.70        45.57        23.44 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18T TCGA-BH-A18U 
       17.26        15.65        30.35        72.56         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       51.16        91.99       114.15        26.14        38.60        57.83 
TCGA-BH-A209 TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW 
      130.16        13.25        12.03        21.83        14.50        12.66 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15R TCGA-E2-A1AZ 
       16.54        14.14        27.12        23.34        17.06        60.53 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R6 TCGA-E9-A1RB 
       53.62        33.70        26.56        12.00         2.76        32.09 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1P8 
        0.69         7.13         0.79        28.77        23.11         7.86 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LL-A441 TCGA-OL-A66I 
       22.09        17.49        79.10        72.10        11.44        23.47 
TCGA-PL-A8LZ TCGA-UU-A93S 
        9.93         3.81 

$`11Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      134.40       107.61        79.76        74.40        72.00        35.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       35.47        30.61        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 
       23.80        21.73        20.61        22.32        11.34        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        19.99        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       32.05         9.99        10.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 
       14.01        12.00        19.04        13.02        21.04        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV 
       19.79        23.24        24.79         1.55        13.71        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.62         2.96         1.71         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.96         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.72       106.78       108.03        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        17.79        24.79        26.93         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91        19.20       111.32        73.64 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        74.79        86.66        42.35        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
       87.22        97.84        76.01        53.36        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        89.00        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       220.90       129.57        50.70       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52       139.17       170.17        85.35        74.99 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       25.71        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.69        53.95        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       44.02        48.13        42.90        45.83        31.17        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       22.13        13.91        48.23         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       69.93       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       28.14        83.31        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66         0.39         3.16         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.12         1.05         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       11.90        20.88        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        18.90        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        19.92        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ 
       15.85        16.31         6.35        12.99        15.16        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         9.93        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        0.76        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        18.51        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
        9.04        20.58        11.05        13.02        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
        5.52        15.72         8.28        30.61        34.92        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       12.85        34.82        32.88        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        3.02        21.21        32.09        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       12.53        13.32        39.09        22.75        41.03        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       23.51        20.71        17.06        27.22         1.94        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        29.72         0.76        26.07        18.41        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       15.72        12.33        23.84        14.70        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       25.91        34.03        10.16        23.51         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       216.76        83.34        75.02        70.85        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 
       13.22         7.10        13.28        10.62        24.95        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       25.05        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG 
       64.21        86.96         0.16         0.26        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.84        13.94        17.03        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.33               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            130.16             234.28 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             23.39              24.69 
[1] "0.3 - 130.2 (23.4)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.6"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         9        5        1        1        34        22
  11Q GAIN WILD-TYPE      80       76        7        2       319       223
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          9          3          4        2
  11Q GAIN WILD-TYPE         2        141         26         59       18
                    vv
clus                 STAGE TIS STAGE X
  11Q GAIN MUTATED           1       1
  11Q GAIN WILD-TYPE         0      12
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  5                 76
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA                34                319
  STAGE IIB                22                223
  STAGE III                 0                  2
  STAGE IIIA                9                141
  STAGE IIIB                3                 26
  STAGE IIIC                4                 59
  STAGE IV                  2                 18
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    22  57   8   4
  11Q GAIN WILD-TYPE 250 559 122  36
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               22                250
  T2               57                559
  T3                8                122
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    47  32   7   5
  11Q GAIN WILD-TYPE 454 318 110  70
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               47                454
  N1               32                318
  N2                7                110
  N3                5                 70
[1] 4 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    81   2
  11Q GAIN WILD-TYPE 798  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     81    2
  11Q GAIN WILD-TYPE  798   19
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               81                798
  1                2                 19
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    91   1
  11Q GAIN WILD-TYPE 960  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     91    1
  11Q GAIN WILD-TYPE  960   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               91                960
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q GAIN MUTATED                            0                            75
  11Q GAIN WILD-TYPE                          1                           688
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q GAIN MUTATED                                4                   2
  11Q GAIN WILD-TYPE                            188                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q GAIN MUTATED                       1                                2
  11Q GAIN WILD-TYPE                     3                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11Q GAIN MUTATED                    1              7
  11Q GAIN WILD-TYPE                 16             41
D22V8, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  75                688
  INFILTRATING LOBULAR CARCINOMA                  4                188
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  7                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    24  68
  11Q GAIN WILD-TYPE 264 706
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     24   68
  11Q GAIN WILD-TYPE  264  706
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                24                264
  YES               68                706
[1] 2 2
[1] FALSE
D22V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                1    59
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          16    66
  11Q GAIN WILD-TYPE                       154   670
D22V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 59
  BLACK OR AFRICAN AMERICAN                      16                154
  WHITE                                          66                670
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  75
  11Q GAIN WILD-TYPE  34 783
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   75
  11Q GAIN WILD-TYPE   34  783
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO               75                783
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   195  28
  12P GAIN WILD-TYPE 721 100
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               223                821 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                100 
$`12P GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      129.14        48.10        39.32        28.01        19.20        18.02 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D0 
       73.84        87.25        75.55         5.19        56.81        67.33 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0YE TCGA-A2-A0YH 
       35.05        34.29        31.82        63.29        18.21        21.67 
TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XW TCGA-A7-A0CD 
       31.73        17.36        19.20        33.93        49.48        38.30 
TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD 
       35.31        29.79        20.19        25.15        20.61        22.32 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.70        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A07U 
        9.37        10.42        53.98         9.01         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
        9.99        45.07        19.96        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 
       30.97         9.99         1.02         1.02        14.01        12.00 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X 
       27.02         2.37        26.04        33.04        16.57        13.71 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0FJ TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX 
        0.33         1.78         7.96         7.04         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J2 
        0.33         0.33        80.28        66.77        95.70        32.78 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12E TCGA-AO-A12F 
       20.32        53.03        72.00       102.58        57.30        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0U2 
       61.87         0.53         5.65        32.91        73.64        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q 
       85.97        51.25        43.07        61.28       160.90       104.28 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LM TCGA-AR-A2LR 
       85.35        50.96        79.00        89.00        52.11        20.38 
TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY 
       54.74       143.38       110.14       162.05        79.63       113.79 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU 
      186.48        43.59        73.51        74.99        68.12        24.53 
TCGA-BH-A0AV TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL 
       59.84        48.36        51.68        37.22        24.85        44.05 
TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0E0 TCGA-BH-A0E7 TCGA-BH-A0EB 
       45.57        44.02        45.83         4.41        44.81        24.49 
TCGA-BH-A0GY TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N 
       30.35        27.25        23.05        90.84        26.66        37.74 
TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       37.55        51.16        91.99        42.28        12.00        55.69 
TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A5IZ TCGA-BH-A5J0 
      114.15        45.63        26.14        38.60        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A130 
        9.63        18.87        11.93        12.66        12.66         3.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 
       12.03         2.30         8.28         9.50        20.88        14.17 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JL TCGA-D8-A1JM 
       19.20        14.17        15.78        18.15        20.09        19.40 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       17.16        21.83        12.99        16.54        15.32        15.52 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A109 
       13.48        10.09        12.26        18.51        34.42        46.59 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A 
       37.51        40.11        44.68        32.02        27.12        23.34 
TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1II 
       18.21        13.02        14.07        60.53        33.73        33.70 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       43.04        16.93         8.28        13.48        12.00        13.12 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RG 
       35.24         9.86         2.76        32.09        40.24        21.27 
TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1J6 
       41.03        17.06        27.22         0.72        29.72        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GI-A2C9 
       22.82        29.82        23.11         7.86        25.91       109.87 
TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A7W5 
       75.02        85.15        69.30         2.60        21.24         7.10 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV 
       24.95        11.44        22.26         2.63        14.70        34.92 
TCGA-OL-A5RZ TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-UL-AAZ6 
       22.32        17.36        16.50        13.12        15.39        17.03 
TCGA-Z7-A8R5 
      108.07 

$`12P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68        31.79         7.96        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       78.41       121.94        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25        98.99       107.93        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       79.76        74.40        72.00        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       20.75        32.55        25.28        50.47        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        23.77        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        83.01        29.98        32.75        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.14        21.90        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H 
       37.45        35.67        33.11        31.73        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY 
       31.36        24.26        23.74        23.80        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VY TCGA-A8-A06O 
       17.92        10.72        11.05        10.29         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        17.03        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        7.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       38.01        28.96        33.01        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
        0.99       112.08        43.00        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       41.98        12.00         9.99        12.00        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        19.04        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70         0.92         2.27        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       22.19        14.99        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       11.44        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        6.28         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       61.35        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       21.40        52.18        26.04        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
      108.03        90.58        98.27        64.04        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
      130.09        15.62        32.52         2.56        19.20       111.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        74.79        86.66        42.35        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH 
       55.86       107.24        65.36       101.95       114.02        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       61.84        52.77        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        17.23        37.81        76.21        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        2.76        87.22        97.84        76.01        53.36        83.77 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        62.86        54.21        66.15        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       40.54        16.04        20.45        10.59        77.62       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       176.98        18.77       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       172.96       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      131.21       157.41        97.48       188.68        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.57       129.70        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW 
      139.17       170.17        85.35       103.63        71.15        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       56.94        56.98        32.02        18.21        25.71        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        11.67        49.05        41.75        48.13        42.90 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       47.41        16.27        15.68        14.30         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       44.81         8.81         2.01         7.23        20.12        72.56 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        55.63        66.05         7.36        51.39        69.93 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
      113.82        82.85        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       72.07        28.14        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 
        6.44        20.12        10.52       109.28         8.94         5.26 
TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P 
        9.70        21.76         9.44        11.77        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        12.66         0.39         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN 
       10.92        11.34        11.28         0.16        10.42         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.23         0.36         0.43         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        11.90        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.97        13.48        21.14        17.49        16.50        18.71 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.12        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15        12.39        15.22        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        15.55        16.41        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        12.66         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        4.80         0.76        13.08        12.53        33.37        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       16.18         8.02        12.10        43.00        27.52        40.41 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        33.30        43.33        34.26        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        25.41        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        22.82        17.29        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.78        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC 
       12.85        34.82        32.88        36.82        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       12.59        35.77        25.84        11.90        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD 
        2.56         6.12         3.02        21.21        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
       20.71         0.69         1.94         7.13        24.56         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.79        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       39.78        52.96        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        52.73        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       23.51         7.40        59.57       216.76        79.10        83.34 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        72.10        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U 
       13.55        18.12        62.43        11.84        11.57        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       13.28        10.62        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.70        14.47        14.79        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        26.04        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.16         0.26         9.93        16.93        16.80        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G 
       15.35        14.96        13.84        13.94         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       107.05 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.33               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            186.48             234.28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             25.91              23.90 
[1] "0.3 - 186.5 (25.9)" "0.0 - 234.3 (23.9)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        18       15        1        2        77        43
  12P GAIN WILD-TYPE      71       66        7        1       276       202
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           0         36          6         18        5
  12P GAIN WILD-TYPE         2        114         23         45       15
                    vv
clus                 STAGE TIS STAGE X
  12P GAIN MUTATED           0       3
  12P GAIN WILD-TYPE         1      10
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 15                 66
  STAGE IB                  1                  7
  STAGE II                  2                  1
  STAGE IIA                77                276
  STAGE IIB                43                202
  STAGE III                 0                  2
  STAGE IIIA               36                114
  STAGE IIIB                6                 23
  STAGE IIIC               18                 45
  STAGE IV                  5                 15
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    45 146  25   9
  12P GAIN WILD-TYPE 227 470 105  31
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               45                227
  T2              146                470
  T3               25                105
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED   108  63  29  21
  12P GAIN WILD-TYPE 393 287  88  54
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              108                393
  N1               63                287
  N2               29                 88
  N3               21                 54
[1] 4 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   190   5
  12P GAIN WILD-TYPE 689  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    190    5
  12P GAIN WILD-TYPE  689   16
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              190                689
  1                5                 16
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   221   5
  12P GAIN WILD-TYPE 830   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    221    5
  12P GAIN WILD-TYPE  830    6
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE              221                830
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P GAIN MUTATED                            1                           178
  12P GAIN WILD-TYPE                          0                           585
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P GAIN MUTATED                               27                   2
  12P GAIN WILD-TYPE                            165                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P GAIN MUTATED                       0                                8
  12P GAIN WILD-TYPE                     4                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12P GAIN MUTATED                    1              8
  12P GAIN WILD-TYPE                 16             40
D23V8, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 178                585
  INFILTRATING LOBULAR CARCINOMA                 27                165
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 22
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  8                 40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    70 156
  12P GAIN WILD-TYPE 218 618
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     70  156
  12P GAIN WILD-TYPE  218  618
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                70                218
  YES              156                618
[1] 2 2
[1] FALSE
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     9
  12P GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          40   155
  12P GAIN WILD-TYPE                       130   581
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      40                130
  WHITE                                         155                581
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5 183
  12P GAIN WILD-TYPE  33 675
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  183
  12P GAIN WILD-TYPE   33  675
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 33
  NOT HISPANIC OR LATINO              183                675
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   164  24
  12Q GAIN WILD-TYPE 752 104
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               188                856 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                104 
$`12Q GAIN MUTATED`
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A0CS 
       39.32        28.01        19.20        18.02        87.25        75.55 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SW 
       56.81        67.33        35.05        34.29        31.82        44.88 
TCGA-A2-A0T7 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E 
       20.75        21.67        17.36        19.20        42.44       105.34 
TCGA-A2-A3XW TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD 
       49.48        38.30        29.79        25.15        20.61        22.32 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A8-A06R TCGA-A8-A06T 
       14.70        13.74        21.17        14.73        17.98        53.06 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z 
       53.98         9.01        10.98         8.98         9.99        45.07 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        33.01        30.97         9.99 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23E 
        1.02        45.07         1.02        14.01        12.00         2.37 
TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0FF 
        5.72        26.04        16.57        13.71         0.33         5.65 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        7.04         0.36         0.33        80.28        66.77        95.70 
TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A12E TCGA-AO-A1KQ 
       32.78        20.32        53.03        72.00        57.30        61.87 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0U2 
        0.53         5.65        32.91        73.64         5.26        83.87 
TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W 
       51.25        61.28        96.89       104.28        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0IO TCGA-B6-A0RO 
       79.00        89.00        52.11        54.74       110.14       162.05 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 
       79.63       113.79       186.48        43.59        73.51        68.12 
TCGA-BH-A0AU TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW 
       24.53        48.36        37.22        44.05        45.57        11.67 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H7 
       44.02        45.83        44.81        24.49        30.35        23.08 
TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R 
       27.25        23.05        90.84        26.66        37.74        37.55 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A5J0 
       42.28        12.00        55.69       114.15        45.63        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A130 TCGA-C8-A138 
        9.63        18.87        11.93        12.66         3.16         4.08 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A1J8 
       11.28        12.03         8.28         9.50        20.88        14.17 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XU 
       15.78        18.15        18.90        17.16        21.83        12.99 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 
       16.54        15.32        13.48        10.09        12.26        18.51 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14W 
       34.42        46.59        37.51        40.11        44.68        32.02 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1IH 
       27.12        23.34        18.21        13.02        14.07        33.73 
TCGA-E2-A1II TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 
       33.70        39.62        43.04         8.28        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC 
       13.12        35.24         9.86         2.76        32.09        40.24 
TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-EW-A1J6 
       41.03        27.22         0.72        29.72        23.84        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A2FV TCGA-GM-A2DI TCGA-HN-A2NL 
       22.82        29.85        23.11        25.91        85.15         2.60 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A740 
       21.24         7.10        15.32        22.26         2.63        14.50 
TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 
       14.70        34.92        17.36        16.50        13.12        15.39 
TCGA-UL-AAZ6 TCGA-Z7-A8R5 
       17.03       108.07 

$`12Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
       18.21       104.81        78.41       121.94        73.84        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       72.00        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.90        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        31.73        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       35.67        33.11        31.73        20.19        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY 
       31.36        24.26        23.74        23.80        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        17.92        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B 
       29.03        31.00        26.01         1.02        17.03        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        9.99         7.99        24.99        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       13.02         0.99        38.01        28.96        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       33.01        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       50.04        49.05        29.98        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       19.04        15.02         0.99        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
        0.99        27.02        17.03        38.04         0.95        10.85 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        50.70        33.04         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
       16.31        14.83        22.19        14.99        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55        11.44        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX 
        7.00         7.59         7.17         6.28         0.33         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       81.63        68.75        47.87        58.95        29.13        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       52.18        26.04        37.48        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
      108.03        90.58        98.27        64.04        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       28.37        14.73        82.62        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        74.79        86.66        42.35        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       75.55        61.84        52.77        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        33.73       160.90        50.89        94.22 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       78.51        84.20         2.76        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       53.36        83.77        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        20.38        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.47       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88       101.52       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35        74.99       103.63        71.15        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       24.85        21.70        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.69        53.95        49.94        49.05        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
        9.63        46.19        32.58        31.00        24.43        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       72.56        30.28        55.63        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX 
       51.16        69.93        91.99       113.82        82.85        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 
       20.12        10.52       109.28         8.94        18.64         5.26 
TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P 
        9.70        21.76         9.44        11.77        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        2.24         1.87         1.12         1.05         4.11        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34         0.16        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.23         0.36         0.43         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        11.90        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        18.71        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       25.74        23.90        27.58        18.15        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        14.50        19.92        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       15.85        16.31         6.35        15.16        12.66        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.53        33.37        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       12.10        43.00        27.52        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        28.60        18.51        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        11.05        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.87       106.75       102.61         8.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        36.82        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.77        25.84        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE 
        6.12         3.02        21.21        32.09         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.71        17.06         0.69         1.94         7.13        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.79        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        25.94        29.95        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.43        11.84        11.57        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        11.44        10.95        25.05        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 
       14.47        14.79        16.08        15.68         7.46        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.73        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        40.08        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       41.92        42.77        26.04        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         9.93        16.93        16.80        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       14.96        13.84        13.94         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.33               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            186.48             234.28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            24.840             24.495 
[1] "0.3 - 186.5 (24.8)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED        14       12        0        1        59        36
  12Q GAIN WILD-TYPE      75       69        8        2       294       209
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           0         39          6         15        5
  12Q GAIN WILD-TYPE         2        111         23         48       15
                    vv
clus                 STAGE TIS STAGE X
  12Q GAIN MUTATED           0       2
  12Q GAIN WILD-TYPE         1      11
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  14                 75
  STAGE IA                 12                 69
  STAGE IB                  0                  8
  STAGE II                  1                  2
  STAGE IIA                59                294
  STAGE IIB                36                209
  STAGE III                 0                  2
  STAGE IIIA               39                111
  STAGE IIIB                6                 23
  STAGE IIIC               15                 48
  STAGE IV                  5                 15
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    35 123  23   9
  12Q GAIN WILD-TYPE 237 493 107  31
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               35                237
  T2              123                493
  T3               23                107
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    76  59  31  18
  12Q GAIN WILD-TYPE 425 291  86  57
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               76                425
  N1               59                291
  N2               31                 86
  N3               18                 57
[1] 4 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   161   5
  12Q GAIN WILD-TYPE 718  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    161    5
  12Q GAIN WILD-TYPE  718   16
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              161                718
  1                5                 16
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   185   5
  12Q GAIN WILD-TYPE 866   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    185    5
  12Q GAIN WILD-TYPE  866    6
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE              185                866
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q GAIN MUTATED                            0                           149
  12Q GAIN WILD-TYPE                          1                           614
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q GAIN MUTATED                               25                   1
  12Q GAIN WILD-TYPE                            167                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q GAIN MUTATED                       0                                9
  12Q GAIN WILD-TYPE                     4                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12Q GAIN MUTATED                    1              4
  12Q GAIN WILD-TYPE                 16             44
D24V8, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 149                614
  INFILTRATING LOBULAR CARCINOMA                 25                167
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  4                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    59 131
  12Q GAIN WILD-TYPE 229 643
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     59  131
  12Q GAIN WILD-TYPE  229  643
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                59                229
  YES              131                643
[1] 2 2
[1] FALSE
D24V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     9
  12Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          33   125
  12Q GAIN WILD-TYPE                       137   611
D24V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      33                137
  WHITE                                         125                611
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4 151
  12Q GAIN WILD-TYPE  34 707
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  151
  12Q GAIN WILD-TYPE   34  707
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO              151                707
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    77  13
  13Q GAIN WILD-TYPE 839 115
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                90                954 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                115 
$`13Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0YJ TCGA-A2-A1FW 
       31.79        73.84        35.05        63.29        18.61        17.36 
TCGA-A2-A1G1 TCGA-A7-A0DA TCGA-A7-A26F TCGA-A7-A3J0 TCGA-A8-A07R TCGA-A8-A08G 
       19.20        35.67        24.26        10.29         8.98        19.96 
TCGA-A8-A08J TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09C TCGA-AC-A2FM 
       37.05        33.01        41.98        12.00         1.02        26.04 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ 
        0.33         0.23         0.33         7.04         0.36         0.33 
TCGA-AN-A0XO TCGA-AO-A03U TCGA-AO-A0J7 TCGA-AO-A0JB TCGA-AO-A12A TCGA-AO-A12B 
       12.33        58.95        20.32        50.70        90.58        98.27 
TCGA-AO-A12D TCGA-AR-A0TT TCGA-AR-A0U3 TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A2LR 
       64.04        86.66       114.02        53.36        89.00        20.38 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0WY TCGA-BH-A0B9 
      110.14       211.56       162.05       100.70       113.79        51.68 
TCGA-BH-A0BT TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18N TCGA-BH-A18V 
       45.57        14.30        24.49        36.85        37.74        51.16 
TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A12L 
       49.58        72.07        57.83        18.64         5.26        11.93 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A1JF TCGA-D8-A1XF 
        2.24         1.12         0.03        20.58        12.03        15.22 
TCGA-D8-A1XJ TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A14Y 
       21.83        10.09        12.26        33.30        31.96        28.60 
TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A1BD TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A574 
       19.43        20.71        17.10        19.66       106.75        26.56 
TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RF TCGA-E9-A248 
       12.00        12.59        35.24         2.56         6.58         1.94 
TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P7 TCGA-EW-A2FV TCGA-EW-A423 TCGA-JL-A3YX 
        0.79        28.77        30.08        25.91        10.16        11.57 
TCGA-LD-A7W5 TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-MS-A51U TCGA-S3-A6ZG TCGA-UU-A93S 
        7.10         2.63        15.68        22.39        13.12         3.81 

$`13Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        13.68         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       72.00        34.29        31.82        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.90        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       23.61        29.56        31.36        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00         9.99        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A099 
      112.08        43.00        40.01        30.97        17.95         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC 
       26.04        37.48        22.36        53.03        21.53        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      108.03        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       42.35        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      101.95        83.87        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       62.14        33.73       160.90        50.89        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       76.01        85.35        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.93       140.88        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       172.96       102.77       140.48        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.88        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        74.99        68.12       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA 
       39.55        39.16        48.36        56.94        56.98        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        46.19        32.58        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        13.61        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        45.63       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       72.07        28.14        26.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         9.70        18.87        21.76         9.44 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        12.66         0.39         3.16         1.87 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         9.50        12.20         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15        12.39        17.16        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
        6.35        12.99        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 
       33.17        43.33        34.26        32.02        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       27.12        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        33.01        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI 
       39.62        24.59        40.47        28.90        18.87       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE 
       36.82        13.48        13.12        36.56        39.55        35.77 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       25.84         9.86        11.90        28.27        34.95         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        34.65        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       12.89        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56         0.72        29.72         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41        30.18        15.72        12.33        23.84        14.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       13.81        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        23.11        18.48         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       23.51         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
        2.60        62.43        11.84        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       15.32        14.70        14.47        14.79        22.26        16.08 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        7.46        14.50        14.70        12.36        14.73        14.07 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        16.50        16.93        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G 
       15.35        14.96        13.84        13.94        17.03        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.03               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            211.56             234.28 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            20.645             24.720 
[1] "0.0 - 211.6 (20.6)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.3"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         6        4        0        0        35        16
  13Q GAIN WILD-TYPE      83       77        8        3       318       229
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           0         17          2          5        2
  13Q GAIN WILD-TYPE         2        133         27         58       18
                    vv
clus                 STAGE TIS STAGE X
  13Q GAIN MUTATED           0       2
  13Q GAIN WILD-TYPE         1      11
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   6                 83
  STAGE IA                  4                 77
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                35                318
  STAGE IIB                16                229
  STAGE III                 0                  2
  STAGE IIIA               17                133
  STAGE IIIB                2                 27
  STAGE IIIC                5                 58
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    18  60   7   4
  13Q GAIN WILD-TYPE 254 556 123  36
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               18                254
  T2               60                556
  T3                7                123
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    42  27  14   7
  13Q GAIN WILD-TYPE 459 323 103  68
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               42                459
  N1               27                323
  N2               14                103
  N3                7                 68
[1] 4 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    81   2
  13Q GAIN WILD-TYPE 798  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     81    2
  13Q GAIN WILD-TYPE  798   19
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               81                798
  1                2                 19
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    90   0
  13Q GAIN WILD-TYPE 961  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     90    0
  13Q GAIN WILD-TYPE  961   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               90                961
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q GAIN MUTATED                            0                            73
  13Q GAIN WILD-TYPE                          1                           690
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q GAIN MUTATED                                4                   0
  13Q GAIN WILD-TYPE                            188                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q GAIN MUTATED                       2                                2
  13Q GAIN WILD-TYPE                     2                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  13Q GAIN MUTATED                    2              7
  13Q GAIN WILD-TYPE                 15             41
D25V8, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  73                690
  INFILTRATING LOBULAR CARCINOMA                  4                188
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  7                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    29  61
  13Q GAIN WILD-TYPE 259 713
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     29   61
  13Q GAIN WILD-TYPE  259  713
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                29                259
  YES               61                713
[1] 2 2
[1] FALSE
D25V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     6
  13Q GAIN WILD-TYPE                                1    54
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                          11    66
  13Q GAIN WILD-TYPE                       159   670
D25V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 54
  BLACK OR AFRICAN AMERICAN                      11                159
  WHITE                                          66                670
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  71
  13Q GAIN WILD-TYPE  32 787
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   71
  13Q GAIN WILD-TYPE   32  787
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO               71                787
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED   125  16
  14Q GAIN WILD-TYPE 791 112
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               141                903 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                112 
$`14Q GAIN MUTATED`
TCGA-A2-A0D2 TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A25C TCGA-A2-A3KD 
       33.76        49.84        21.67        17.36        17.19        39.65 
TCGA-A2-A4RX TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A56D TCGA-A8-A075 TCGA-A8-A076 
       24.39        30.61        33.11        14.73        17.03        53.98 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 
       38.01        12.00        33.01        33.01        30.97        41.98 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 
        9.99         1.02        33.07         8.98        14.01        19.04 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM TCGA-AC-A62Y TCGA-AN-A04A TCGA-AN-A0FW 
       27.02         2.37        26.04        17.42         2.96         0.36 
TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A0J7 
        0.33        80.28        66.77        81.63        95.70        20.32 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24R 
       72.00        76.77        71.80        50.89        96.89        87.22 
TCGA-AR-A250 TCGA-AR-A2LK TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0RO 
       89.00        54.21        54.74       149.59       129.57       162.05 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KN 
      100.70       131.21        79.63       113.79       129.57       139.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT 
       85.35        68.12        37.22        44.05        48.69        45.57 
TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0HI 
       23.44        48.23         2.56        46.19        31.00        20.38 
TCGA-BH-A0HX TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV 
       27.25        44.81        90.84        26.66        69.93        12.00 
TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12O TCGA-C8-A12P 
       45.63        72.07        23.51         5.26        12.66        11.77 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A27A TCGA-D8-A13Z 
        3.16         1.87         4.08        11.28        12.20        20.88 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF 
       20.58        14.17        21.14        14.17        18.15        12.03 
TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XZ TCGA-D8-A27W 
       20.12        18.58        15.22        19.92        15.32        12.26 
TCGA-D8-A3Z6 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A152 TCGA-E2-A153 
       18.51        46.59        40.11        40.96        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A1L9 
       19.43        20.71        18.21        17.42         9.04        19.66 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A9RU TCGA-E9-A1NF TCGA-E9-A1NI 
       18.87        43.04        16.93        12.85        35.24         9.86 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A22E 
       40.24        34.65         6.58        34.59        41.03        12.89 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY 
        0.69        27.22         0.72         0.79        14.40         8.48 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1PG TCGA-EW-A2FS TCGA-GM-A2DB TCGA-LL-A5YM 
       40.41        52.96        34.55        52.73        79.10        15.32 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A6VR 
       14.47         2.63        14.73        22.39        36.36        40.11 
TCGA-S3-A6ZG TCGA-WT-AB44 TCGA-Z7-A8R6 
       13.12        29.03       107.05 

$`14Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       98.99       107.93        56.81        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13         8.38        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.90        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        23.47        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15       105.34        10.59        20.88        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        49.48        47.31        34.98        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37         7.30        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.90        38.30        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        29.79        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        17.92        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       13.02         0.99        28.96        33.01        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       40.01        17.95        12.00         9.99        12.00        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       49.05        45.07        29.98         1.02        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        12.00        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55        11.44        13.71        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         1.78         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
        5.59        61.35        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       32.78        21.40        52.18        26.04        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG 
       53.03        21.53        50.70        50.86        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      111.32        73.64         5.26        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O 
       62.14        33.73       160.90        94.22        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       104.28        97.84        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        79.00        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       58.92        93.83       143.21        20.25        62.86        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       52.11        38.17        39.39        40.54        20.38        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       18.35        21.47       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A402 
       58.88        43.59       101.52        73.51       170.17        74.99 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       24.85        21.70        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        42.90        45.83        31.17        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        17.26        15.65         3.22        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        32.58        24.49        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.66       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59        28.14        26.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
        8.94        18.64         9.63         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66        12.66         0.39         2.24         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        1.05         4.11        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50         0.99         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A145 
       13.41        19.46        11.90        13.25        13.97        13.48 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        18.71        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        18.97        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.66        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       12.53        33.37        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       18.51        25.41        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        12.92        19.40 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       20.98        11.08        54.18        27.42        39.62        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       40.47        28.90       106.75       102.61         8.75         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       15.72         8.28        30.61        34.92        26.56        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       36.56        39.55        12.59        35.77        25.84        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI 
       21.21        32.09        32.09         1.12        21.27        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       23.51        20.71        17.06         1.94         7.13        24.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        23.84        14.70        13.81        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       28.77        25.94        22.82        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.43        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       25.05        17.06        14.70        14.79        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 
       15.68         7.46        14.50        14.70        12.36        14.07 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        14.07        28.21        19.73         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       15.35        16.04       108.07 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.33               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            162.05             234.28 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.66              24.49 
[1] "0.3 - 162.1 (26.7)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         9        8        1        0        47        29
  14Q GAIN WILD-TYPE      80       73        7        3       306       216
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           1         27          4         10        1
  14Q GAIN WILD-TYPE         1        123         25         53       19
                    vv
clus                 STAGE TIS STAGE X
  14Q GAIN MUTATED           0       2
  14Q GAIN WILD-TYPE         1      11
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  8                 73
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                47                306
  STAGE IIB                29                216
  STAGE III                 1                  1
  STAGE IIIA               27                123
  STAGE IIIB                4                 25
  STAGE IIIC               10                 53
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    29  92  15   5
  14Q GAIN WILD-TYPE 243 524 115  35
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               29                243
  T2               92                524
  T3               15                115
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    60  43  24  11
  14Q GAIN WILD-TYPE 441 307  93  64
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               60                441
  N1               43                307
  N2               24                 93
  N3               11                 64
[1] 4 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   121   1
  14Q GAIN WILD-TYPE 758  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    121    1
  14Q GAIN WILD-TYPE  758   20
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0              121                758
  1                1                 20
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   141   0
  14Q GAIN WILD-TYPE 910  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    141    0
  14Q GAIN WILD-TYPE  910   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE              141                910
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q GAIN MUTATED                            0                           109
  14Q GAIN WILD-TYPE                          1                           654
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q GAIN MUTATED                               15                   0
  14Q GAIN WILD-TYPE                            177                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q GAIN MUTATED                       2                                8
  14Q GAIN WILD-TYPE                     2                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  14Q GAIN MUTATED                    2              5
  14Q GAIN WILD-TYPE                 15             43
D26V8, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 109                654
  INFILTRATING LOBULAR CARCINOMA                 15                177
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 22
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  5                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    41 100
  14Q GAIN WILD-TYPE 247 674
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     41  100
  14Q GAIN WILD-TYPE  247  674
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                41                247
  YES              100                674
[1] 2 2
[1] FALSE
D26V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     9
  14Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          23    93
  14Q GAIN WILD-TYPE                       147   643
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      23                147
  WHITE                                          93                643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2 115
  14Q GAIN WILD-TYPE  36 743
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  115
  14Q GAIN WILD-TYPE   36  743
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 36
  NOT HISPANIC OR LATINO              115                743
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    77   8
  15Q GAIN WILD-TYPE 839 120
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                85                959 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                120 
$`15Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0EV 
      129.14        48.10        39.32        98.99        33.76        31.82 
TCGA-A2-A0T2 TCGA-A2-A1FW TCGA-A2-A1G4 TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XY 
        8.38        17.36        19.56        17.19        83.01        34.98 
TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A4SE 
       35.31        37.45        25.15        23.74        11.34        21.17 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A07P TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08P 
       13.02         1.02        10.98        24.99        38.01        31.00 
TCGA-A8-A097 TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-AC-A2QH TCGA-AN-A0XU 
       12.00        49.05        29.98        33.07        33.04         0.33 
TCGA-AO-A0J2 TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TP 
       32.78        71.80       102.58        64.04       130.09       111.32 
TCGA-AR-A0U2 TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A254 TCGA-AR-A2LH 
       83.87        61.28        62.14        50.89        72.76        20.25 
TCGA-B6-A0I5 TCGA-B6-A0IM TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DL TCGA-BH-A0DS 
      149.59       126.12        24.85        48.69        48.23         2.56 
TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18V TCGA-BH-A1FH TCGA-BH-A5J0 
       31.00        23.05        37.74        51.16        36.92        23.51 
TCGA-C8-A12O TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Z 
       12.66         1.87        11.28         2.30         0.36         8.28 
TCGA-D8-A1JP TCGA-D8-A27R TCGA-E2-A10A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A1IL 
       21.01        10.09        40.41        17.29        20.71         3.88 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N8 TCGA-E9-A1NF 
       28.90       106.75        43.04         8.28        12.00        35.24 
TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW 
        2.56        32.09        12.33         8.48        28.77        22.82 
TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GM-A2DF TCGA-GM-A2DK TCGA-LL-A5YM TCGA-OL-A5RV 
       23.11        19.99        70.85        86.96        15.32        34.92 
TCGA-PL-A8LX 
        0.16 

$`15Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        61.58        25.22       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       44.88        50.43        44.28        17.52        17.13        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       19.33        48.46        31.73        23.77        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.20        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       42.44        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ 
       33.93        29.98        32.75        49.48        47.31        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        24.26        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       22.32        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        14.50        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       26.01         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        9.99         8.98         7.99         9.99        45.07        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       15.06        36.95        13.02         0.99        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       19.96        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       50.04        45.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         5.72         1.48        38.53        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       95.70        68.75        47.87        58.95        29.13        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        55.33        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
      106.78       108.03        90.58        98.27        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        17.79        24.79        26.93         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56        32.91        19.20        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24        65.36       101.95       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        33.73       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       78.48        73.18        58.92        93.83       143.21        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       176.98        18.77        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
       73.51       139.17       170.17        85.35        74.99        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        38.01        22.13        13.91        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        26.66        72.56        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        33.17        74.73       122.89        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
       20.12        10.52       109.28         8.94        18.64         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66         0.39         3.16         2.24         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.43         9.67         9.53         0.03         9.50        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        0.99         0.03         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
        6.35        12.99        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        18.51        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        33.70        28.44        22.65        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        18.87       102.61         8.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        13.48        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       39.55        12.59        35.77        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       28.27        34.95         6.12         3.02         2.76        21.21 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         1.12        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        22.75        41.03        12.89        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.69        27.22         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        29.72         0.76        26.07        18.41        30.18 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       15.72        23.84        14.70         0.79        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       15.39        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       34.03        17.49        10.16        23.51         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        75.02        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       85.15       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95        25.05        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       64.21        86.96         0.26         9.93        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.16               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            149.59             234.28 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             29.98              23.93 
[1] "0.2 - 149.6 (30.0)" "0.0 - 234.3 (23.9)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED        10        6        0        0        29        17
  15Q GAIN WILD-TYPE      79       75        8        3       324       228
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1         12          2          5        3
  15Q GAIN WILD-TYPE         1        138         27         58       17
                    vv
clus                 STAGE TIS STAGE X
  15Q GAIN MUTATED           0       1
  15Q GAIN WILD-TYPE         1      12
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                  6                 75
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                29                324
  STAGE IIB                17                228
  STAGE III                 1                  1
  STAGE IIIA               12                138
  STAGE IIIB                2                 27
  STAGE IIIC                5                 58
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    23  47  12   3
  15Q GAIN WILD-TYPE 249 569 118  37
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               23                249
  T2               47                569
  T3               12                118
  T4                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    41  27   9   7
  15Q GAIN WILD-TYPE 460 323 108  68
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               41                460
  N1               27                323
  N2                9                108
  N3                7                 68
[1] 4 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    74   3
  15Q GAIN WILD-TYPE 805  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     74    3
  15Q GAIN WILD-TYPE  805   18
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               74                805
  1                3                 18
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    85   1
  15Q GAIN WILD-TYPE 966  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     85    1
  15Q GAIN WILD-TYPE  966   10
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               85                966
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q GAIN MUTATED                            0                            74
  15Q GAIN WILD-TYPE                          1                           689
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q GAIN MUTATED                                3                   0
  15Q GAIN WILD-TYPE                            189                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q GAIN MUTATED                       0                                1
  15Q GAIN WILD-TYPE                     4                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  15Q GAIN MUTATED                    2              5
  15Q GAIN WILD-TYPE                 15             43
D27V8, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  74                689
  INFILTRATING LOBULAR CARCINOMA                  3                189
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  5                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30  56
  15Q GAIN WILD-TYPE 258 718
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30   56
  15Q GAIN WILD-TYPE  258  718
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                30                258
  YES               56                718
[1] 2 2
[1] FALSE
D27V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     8
  15Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                          14    52
  15Q GAIN WILD-TYPE                       156   684
D27V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      14                156
  WHITE                                          52                684
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  68
  15Q GAIN WILD-TYPE  35 790
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   68
  15Q GAIN WILD-TYPE   35  790
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO               68                790
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   392  59
  16P GAIN WILD-TYPE 524  69
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               451                593 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                 69 
$`16P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04N 
       48.10        14.27        20.88        13.68        28.01       104.81 
TCGA-A2-A04P TCGA-A2-A04V TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       18.02        63.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO 
       75.55        56.81        33.76        61.58       101.72        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        34.29        31.82        54.64        27.12        44.88 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YE 
       17.13         8.38        49.84        17.46        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       50.47        21.90        21.67        18.61        23.77        17.36 
TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S2 
       20.25        52.47        47.31        34.98        26.96        21.14 
TCGA-A7-A0CE TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H 
       35.31        33.11        29.79        29.56        31.36        23.80 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        11.97        13.74        21.17        17.92        12.10 
TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       10.42        13.02         1.02        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R 
       26.01         1.02        18.97        12.00        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        0.99        38.01        28.96        33.01        19.96        12.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       31.00        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E 
       17.95        41.98        12.00         9.99        12.00        49.05 
TCGA-A8-A09K TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 
       29.98        19.04        15.02        14.01        12.00         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04         2.37        10.85         1.48 
TCGA-AC-A2FG TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3W5 
       36.99        50.70         0.92        32.45        22.19        16.57 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6NO 
        1.55        11.44        13.71        17.42        18.67         1.68 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.33         0.23         0.62         2.96         1.78 
TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY 
        9.96         0.16         7.00         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.33        12.33         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J7 TCGA-AO-A0J8 
       80.28        66.77        81.63        29.13        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       53.03        76.77        55.33        71.80       102.58        99.25 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H 
       90.58        57.30        82.62        61.87         0.53        24.79 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV 
        5.65        15.62        32.91         5.26        74.79        42.35 
TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AP 
       98.93        83.87        61.84        51.25        48.82        39.98 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24P 
       37.81        61.28        62.14        94.22        78.51         2.76 
TCGA-AR-A24Q TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK 
      104.28        83.77        89.00        72.76        58.92        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 
       66.15        52.11        39.39        54.74        20.45       143.38 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IO 
      129.57        50.70        65.72       146.50       112.37       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      110.93       140.88       234.28        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY 
      102.77       140.48       100.70        97.48       188.68       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 
      129.57       186.48       101.52        73.51        85.35        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP 
       39.55        48.36        37.22        24.85        44.05        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DH 
       27.19        45.57        44.02        48.13        42.90        38.01 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26        15.65         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       47.41        16.27         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H9 
       24.49        31.00        30.35        37.78        24.56        41.00 
TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W5 
       20.38        36.85        12.89        27.25        23.93        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M 
       44.81        23.05         8.81         7.23        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EV 
       37.74        55.63         7.36        51.16        91.99        12.00 
TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FG TCGA-BH-A1FM 
       49.58        31.53        89.16       120.62       122.89        45.63 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A42V TCGA-BH-A5J0 
       72.07        26.14        83.31        57.83         8.94        23.51 
TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W 
        9.63        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK 
        0.39         2.24         1.87         4.08        11.28        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 
        2.30         3.25         0.23         0.43         8.28         9.53 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       13.02        20.88        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       21.14        14.17        17.49        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.03        20.09        20.12        18.58        17.79        16.73 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL 
       27.58        18.15        12.39        15.22        21.83        19.92 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       15.85        16.31        12.99        12.66        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27W 
        9.93        14.24        14.43         9.44        16.41        12.26 
TCGA-D8-A3Z5 TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       33.37        12.10        34.42        40.41        37.51        40.11 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       28.87        44.68        38.24        43.33        34.26        31.96 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C 
       18.51        27.12        23.24        19.43        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M 
       17.29        20.71        18.21        17.42         9.04        11.05 
TCGA-E2-A15O TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       13.02        53.62        32.35        16.47        17.10        37.41 
TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG 
       28.44        20.98        11.08        39.62        19.66        18.87 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N5 
       43.04        16.93         5.52         8.28        30.61        36.82 
TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.00        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09        40.24         1.12        34.65        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
       35.64        34.13        22.75        12.89        20.71        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-E9-A3X8 
        7.13        24.56         0.72        29.72        18.41        15.72 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IY TCGA-EW-A1J3 
       23.84         0.79        14.40        15.39         8.48        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       25.94        22.82        40.41        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 
       18.48        34.55        52.73        34.03         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A3XN 
      216.76        79.10        75.02        85.15       101.62        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-LL-A5YM 
       13.55        18.12        11.57        21.24        17.06        15.32 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A9Q3 
       14.79        22.26         2.63        15.68        14.70        14.07 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX 
       27.91        22.39         2.10        31.99        34.92        28.87 
TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DE TCGA-PL-A8LZ 
       22.32        41.92        26.04        19.73        86.96         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB44 TCGA-Z7-A8R5 
       13.12        16.93        17.03        11.41        29.03       108.07 
TCGA-Z7-A8R6 
      107.05 

$`16P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SH 
       48.36         9.96         8.52        14.37        43.43        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q 
       31.79         7.96        39.32        19.20        18.21        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        87.25       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
      136.73        99.12       107.93        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EP 
      107.93        67.33        34.55        25.22       134.40       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       79.76        74.40        72.00        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T6 
       99.19        50.43        44.28        17.52        20.52        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       20.75        32.55        49.48        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       23.21        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       37.45        35.67        31.73        20.19        25.15        23.61 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SD 
       10.59        10.29        11.28        13.41        14.93        14.50 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.73        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       13.02        53.06        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07U 
       19.99        18.97        14.01        32.05         9.99        24.99 
TCGA-A8-A082 TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X 
       18.05        37.05         9.99        31.00         0.99        43.00 
TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N 
        9.99         1.02        50.04        45.07        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       25.02         8.98         0.99        19.04        13.02        21.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95         5.72        38.53        99.35        40.57        55.43 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        26.04        33.04         2.27        16.31        14.83 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IW TCGA-AC-A6IX 
       14.99        19.79        23.24        24.79        13.58        12.26 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        0.33         1.71         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        6.28         7.04         0.33         0.33         0.30         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        61.35        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        72.00        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B 
       50.24        62.04       108.72       106.78       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       64.04        48.36        41.62        28.37        14.73        70.39 
TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       17.79        26.93       130.09        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      111.32        73.64        86.66        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       101.95       114.02        85.97        75.55        52.77 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       76.11        43.73        43.56        43.07        17.23        76.21 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24O 
       63.62        33.73       160.90        50.89        96.89        84.20 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       87.22        97.84        76.01        53.36        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        78.48        73.18        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QQ 
       62.86        38.17        40.54        20.38        16.04        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK 
       77.62       149.59        12.13       220.90       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      126.12        84.59       211.56        68.45       189.01        81.17 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       131.21       157.41        79.63        18.35        21.47 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
      170.17        74.99        28.50        46.95        40.83        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       21.70        61.68        35.67        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        49.05        41.75        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       22.13        13.91         3.22         4.41        15.68        14.30 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0HA 
       24.43        10.78        15.16        35.51        23.08        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY 
       26.50         5.85         2.50        13.61        51.32        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P 
        5.59        24.95         2.01        20.12        90.84        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05        51.39        69.93       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 
       42.28        55.69        17.69        25.81        97.48        24.66 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        33.17        74.73        36.92        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O 
      144.59        72.07        28.14        38.60       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A6R9 
        6.44        20.12        10.52       109.28        18.64         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12P 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66        12.66         3.16         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.11        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.30         0.36         9.67         0.03         9.50        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.99         0.03         0.23        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       11.90        13.25        19.20        16.50        18.71        15.78 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XD 
       12.20        13.32        14.70        25.74        23.90        17.16 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XT 
       14.73        14.50        17.69        15.55        16.41         6.35 
TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.16        15.52        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       13.05        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 
       12.53        18.51        21.67        16.18         8.02        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R 
       27.52        46.59        28.44        47.15        40.96        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A155 
       33.17        33.30        32.02        28.60        25.41        21.04 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J 
       14.79        25.05        23.34        21.63        12.92        19.40 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       53.03        33.01        28.50        38.30        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A1L7 
       33.70        22.65         3.88        22.19        54.18        27.42 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        40.47        28.90       106.75       102.61         8.75 
TCGA-E2-A3DX TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       15.72        34.92        26.56        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        13.48        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1R2 TCGA-E9-A1RF TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       35.77        34.95         6.58        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       39.09        41.03        23.51        17.06         0.69         1.94 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO 
        0.76        26.07        30.18        12.33        14.70        13.81 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       12.20        39.72        18.21        18.90        13.25        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P7 
       28.77        29.95        29.85        41.13        39.78        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 
       14.43        19.96        55.00        25.91        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       10.16        23.51        59.57        83.34        70.85        72.10 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       86.96       115.69       106.06        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       43.73        69.30        72.03         2.60        62.43        11.84 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z 
       10.95        25.05        14.70        14.47        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5DA 
       14.50        12.36        14.73        36.30        58.52        58.62 
TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       40.08        36.36        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VR 
       65.62        42.77        17.36        14.07        28.21        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF 
        8.91        47.01        64.21         0.16         0.26        16.50 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UU-A93S TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       13.94         3.81        52.96        15.35        16.04 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.16               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            234.28             220.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.49              24.66 
[1] "0.2 - 234.3 (24.5)" "0.0 - 220.9 (24.7)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED        41       33        4        3       144       108
  16P GAIN WILD-TYPE      48       48        4        0       209       137
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           1         67         17         23        9
  16P GAIN WILD-TYPE         1         83         12         40       11
                    vv
clus                 STAGE TIS STAGE X
  16P GAIN MUTATED           1       5
  16P GAIN WILD-TYPE         0       8
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  41                 48
  STAGE IA                 33                 48
  STAGE IB                  4                  4
  STAGE II                  3                  0
  STAGE IIA               144                209
  STAGE IIB               108                137
  STAGE III                 1                  1
  STAGE IIIA               67                 83
  STAGE IIIB               17                 12
  STAGE IIIC               23                 40
  STAGE IV                  9                 11
  STAGE TIS                 1                  0
  STAGE X                   5                  8
[1] 13  2
[1] TRUE
[1] "dimension of 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   113 266  59  18
  16P GAIN WILD-TYPE 159 350  71  22
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              113                159
  T2              266                350
  T3               59                 71
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED   214 150  57  27
  16P GAIN WILD-TYPE 287 200  60  48
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0              214                287
  N1              150                200
  N2               57                 60
  N3               27                 48
[1] 4 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   382   9
  16P GAIN WILD-TYPE 497  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    382    9
  16P GAIN WILD-TYPE  497   12
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              382                497
  1                9                 12
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   452   6
  16P GAIN WILD-TYPE 599   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    452    6
  16P GAIN WILD-TYPE  599    5
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE              452                599
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P GAIN MUTATED                            1                           334
  16P GAIN WILD-TYPE                          0                           429
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P GAIN MUTATED                               86                   2
  16P GAIN WILD-TYPE                            106                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P GAIN MUTATED                       2                               16
  16P GAIN WILD-TYPE                     2                               14
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16P GAIN MUTATED                    2             14
  16P GAIN WILD-TYPE                 15             34
D28V8, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 334                429
  INFILTRATING LOBULAR CARCINOMA                 86                106
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               16                 14
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 14                 34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   122 336
  16P GAIN WILD-TYPE 166 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    122  336
  16P GAIN WILD-TYPE  166  438
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               122                166
  YES              336                438
[1] 2 2
[1] FALSE
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1    23
  16P GAIN WILD-TYPE                                0    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          56   324
  16P GAIN WILD-TYPE                       114   412
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          23                 37
  BLACK OR AFRICAN AMERICAN                      56                114
  WHITE                                         324                412
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    10 361
  16P GAIN WILD-TYPE  28 497
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10  361
  16P GAIN WILD-TYPE   28  497
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   10                 28
  NOT HISPANIC OR LATINO              361                497
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   113  25
  16Q GAIN WILD-TYPE 803 103
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               138                906 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                25                103 
$`16Q GAIN MUTATED`
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A04P TCGA-A2-A0CM TCGA-A2-A0CX 
       14.27        20.88        13.68        18.02        24.79        56.81 
TCGA-A2-A0D2 TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG 
       33.76        35.05        31.82        27.12        44.88        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0DC 
       23.77        17.36        47.31        34.98        26.96        29.79 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A5ZV TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07W 
       14.70        11.97        12.10        26.01         1.02         9.99 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A0A7 TCGA-AC-A3BB TCGA-AC-A62V TCGA-AC-A62Y 
       33.01        12.00         0.99        32.45        11.44        17.42 
TCGA-AC-A6IV TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FY 
       18.67         0.23         0.62         2.96         9.96         0.33 
TCGA-AN-A0XO TCGA-AO-A03V TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A1KQ TCGA-AQ-A54O 
       12.33        29.13        76.77        55.33        61.87        32.91 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A250 
        5.26        74.79        98.93        61.28        62.14        89.00 
TCGA-AR-A255 TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RQ 
       58.92        65.72       110.14        78.02       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 
      100.70       188.68       113.79       101.52        73.51        85.35 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0DL TCGA-BH-A0H6 TCGA-BH-A0H7 
       24.85        44.05        45.57        48.23        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q 
       41.00        42.35         7.23        26.66        72.56        55.63 
TCGA-BH-A18V TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A208 
       51.16        49.58       120.62        72.07        83.31        57.83 
TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A1HK 
        9.63        11.93        12.66         2.24         1.87        12.03 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A8HP TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
        0.43         8.28        13.02        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF 
       21.14        12.03        20.12        16.73        18.15        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27I 
       21.83        12.99        12.66        15.32        14.24        14.43 
TCGA-D8-A27W TCGA-E2-A10F TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15M 
       12.26        28.87        31.96        27.12        19.43        11.05 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IJ TCGA-E2-A1LL TCGA-E9-A1NI TCGA-E9-A1RC 
       53.62        32.35        28.44        43.04         9.86        40.24 
TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 
       22.75        27.22        29.72         0.79        22.82        29.82 
TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A3XN 
       23.11       109.87       216.76        79.10        75.02        66.38 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-OK-A5Q2 
       15.32        14.79         2.63        15.68        14.70         2.10 
TCGA-OL-A5RZ TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-Z7-A8R5 
       22.32        86.96         9.93        16.93        17.03       108.07 

$`16Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        78.41       121.94        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
        5.19        98.99       107.93        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       74.40        72.00        34.29        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        50.43        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        18.21        50.47        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        31.73        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       35.47        30.61        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        10.29        11.28        13.41        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        17.92        14.73        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        53.06        29.03        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J 
       13.02         0.99        38.01        28.96        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
        9.99        31.00        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       43.00        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       19.04        13.02        21.04        27.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         5.72         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70        33.04         0.92         2.27        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
        1.55        13.71        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.33         1.78         1.71         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        58.95        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        72.00        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT 
       32.52         2.56        19.20       111.32        73.64        86.66 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       42.35        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       43.07        17.23        37.81        76.21        63.62        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       85.35        50.96        83.77        79.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        93.83       143.21        20.25        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG 
      149.59        12.13       220.90       129.57        50.70       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       176.98        18.77       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       102.77        89.46       131.21       157.41        97.48 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        18.35        21.47       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59       139.17       170.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       74.99        68.12       103.63        71.15        24.53        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       31.17        23.44        38.01        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HB 
       10.78        15.16        37.78        35.51        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05         8.81         2.01        20.12        90.84 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       69.93        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       55.69        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       26.14        38.60       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 
       10.52       109.28         8.94        18.64        23.51         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        0.39         3.16         1.12         1.05         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
       12.33        10.92        11.34        11.28         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 
        2.30         3.25         0.30         0.23         0.36         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.53         0.03         9.50        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
        0.23        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        20.58        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 
       12.20        13.32        14.70        18.58        17.79        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       23.90        27.58        12.39        17.16        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
        6.35        15.16        16.54        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.45        13.05         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       28.60        18.51        25.41        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       60.53        53.03        33.01        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        33.70        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        21.21        32.09        32.09         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        41.03        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.71        17.06         0.69         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        23.84        14.70        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        52.96        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        34.03        17.49        10.16        23.51         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       43.73        69.30        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z 
       17.06        14.70        14.47        22.26        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        12.36        14.73        14.07        27.91        22.39 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.16         0.26        16.50        13.12        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S 
       13.84        15.35        14.96        13.84        13.94         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       11.41        52.96        29.03        15.35        16.04       107.05 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            216.76             234.28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            24.675             24.510 
[1] "0.2 - 216.8 (24.7)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED        11        7        1        1        42        33
  16Q GAIN WILD-TYPE      78       74        7        2       311       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         25          7          7        4
  16Q GAIN WILD-TYPE         2        125         22         56       16
                    vv
clus                 STAGE TIS STAGE X
  16Q GAIN MUTATED           1       1
  16Q GAIN WILD-TYPE         0      12
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  7                 74
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA                42                311
  STAGE IIB                33                212
  STAGE III                 0                  2
  STAGE IIIA               25                125
  STAGE IIIB                7                 22
  STAGE IIIC                7                 56
  STAGE IV                  4                 16
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    29  81  20   8
  16Q GAIN WILD-TYPE 243 535 110  32
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               29                243
  T2               81                535
  T3               20                110
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    63  44  22   7
  16Q GAIN WILD-TYPE 438 306  95  68
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               63                438
  N1               44                306
  N2               22                 95
  N3                7                 68
[1] 4 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   113   4
  16Q GAIN WILD-TYPE 766  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    113    4
  16Q GAIN WILD-TYPE  766   17
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0              113                766
  1                4                 17
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   136   4
  16Q GAIN WILD-TYPE 915   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    136    4
  16Q GAIN WILD-TYPE  915    7
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE              136                915
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q GAIN MUTATED                            1                           109
  16Q GAIN WILD-TYPE                          0                           654
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q GAIN MUTATED                               17                   1
  16Q GAIN WILD-TYPE                            175                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q GAIN MUTATED                       2                                4
  16Q GAIN WILD-TYPE                     2                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16Q GAIN MUTATED                    1              5
  16Q GAIN WILD-TYPE                 16             43
D29V8, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 109                654
  INFILTRATING LOBULAR CARCINOMA                 17                175
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  5                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    35 105
  16Q GAIN WILD-TYPE 253 669
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     35  105
  16Q GAIN WILD-TYPE  253  669
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                35                253
  YES              105                669
[1] 2 2
[1] FALSE
D29V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     8
  16Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          27    96
  16Q GAIN WILD-TYPE                       143   640
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      27                143
  WHITE                                          96                640
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2 123
  16Q GAIN WILD-TYPE  36 735
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2  123
  16Q GAIN WILD-TYPE   36  735
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 36
  NOT HISPANIC OR LATINO              123                735
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    88  16
  17P GAIN WILD-TYPE 828 112
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               104                940 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                112 
$`17P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A2-A0CX TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
        9.96        13.68        56.81        35.05        34.29        31.82 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A3XU TCGA-A2-A3XX 
       18.61        23.77        60.72        52.47        29.98        47.31 
TCGA-A2-A3XZ TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A8-A07P 
       50.37        38.30        29.79        20.61        10.29        10.98 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09B 
       19.96        37.05        31.00        33.01        12.00        12.00 
TCGA-A8-A09E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A8OP 
       49.05        10.85         5.72        26.04        33.04        20.19 
TCGA-AN-A04A TCGA-AO-A03L TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 
        2.96        80.28        26.04        20.32        55.33       102.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AR-A0TQ TCGA-AR-A1AV TCGA-AR-A1AW 
       98.27        57.30        61.87        73.64        61.28        63.62 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A2LL 
       50.89       104.28        87.22        73.18        54.21        66.15 
TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW 
       21.47        43.59        73.51        85.35        24.53        20.45 
TCGA-BH-A0B4 TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0HQ 
       39.16        24.85        45.57        41.75        42.90        36.85 
TCGA-BH-A0HW TCGA-BH-A18N TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A204 
       51.32        37.74        49.58        25.81       114.15        83.31 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HN TCGA-D8-A143 
       12.66         3.16         1.87        11.28         3.25        14.17 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A27W 
       18.71        12.03        20.09        18.15        16.31        12.26 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A1B1 
       34.42        46.59        44.68        33.30        32.02        53.03 
TCGA-E2-A1B5 TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1QZ TCGA-E9-A1R6 TCGA-E9-A1RH 
       32.35         8.75        26.56        11.90         2.76        34.59 
TCGA-E9-A22E TCGA-E9-A54Y TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A2FS 
       12.89        23.84        29.95        29.85         6.15        52.73 
TCGA-GM-A2DK TCGA-HN-A2NL TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OL-A66K 
       86.96         2.60        14.79        14.70        22.39        41.92 
TCGA-OL-A6VO TCGA-S3-A6ZG 
       28.21        13.12 

$`17P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        98.99       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ 
       19.33        48.46        31.73        23.47        17.36        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.20        19.56        16.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 
       33.93        83.01        32.75        49.48        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       22.32        11.34        10.59        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S 
       14.01        12.00        32.05         9.99         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       13.02         0.99        38.01        28.96        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        50.04        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         2.37         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       99.35        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22         0.03         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        0.33         0.33         0.23         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80        99.25       108.72       106.78       108.03        90.58 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32         5.26        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       17.23        37.81        76.21        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S 
       94.22        96.89        78.51        84.20         2.76        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        78.48        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        62.86        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        79.63        18.35       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        74.99        68.12       103.63        71.15 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       48.36        56.94        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        44.02        48.13        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28         8.94        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         0.39         2.24         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        10.42         2.30         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       12.20         0.99         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        27.58        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       12.10        43.00        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.17        43.33        34.26        31.96        28.60        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       25.41        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        60.53        53.62        33.01        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90        18.87       106.75       102.61        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
        5.52        15.72         8.28        30.61        34.92        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       12.85        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       25.84         9.86        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02        21.21        32.09        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        21.27        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        41.03        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       20.71        17.06         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.18        15.72        12.33        14.70         0.79        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       22.82        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        70.85        72.10        85.15       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        12.36        14.73        14.07        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        23.47        65.62        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       86.96         0.16         0.26         9.93        16.50        16.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.87               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            114.15             234.28 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             31.41              23.51 
[1] "1.9 - 114.2 (31.4)" "0.0 - 234.3 (23.5)"
[1] "hr=" "1.5"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         7        6        0        0        38        23
  17P GAIN WILD-TYPE      82       75        8        3       315       222
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1         19          6          2        2
  17P GAIN WILD-TYPE         1        131         23         61       18
                    vv
clus                 STAGE TIS STAGE X
  17P GAIN MUTATED           0       0
  17P GAIN WILD-TYPE         1      13
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   7                 82
  STAGE IA                  6                 75
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                38                315
  STAGE IIB                23                222
  STAGE III                 1                  1
  STAGE IIIA               19                131
  STAGE IIIB                6                 23
  STAGE IIIC                2                 61
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of 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    23  57  15   9
  17P GAIN WILD-TYPE 249 559 115  31
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               23                249
  T2               57                559
  T3               15                115
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED    45  37  17   3
  17P GAIN WILD-TYPE 456 313 100  72
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               45                456
  N1               37                313
  N2               17                100
  N3                3                 72
[1] 4 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    91   2
  17P GAIN WILD-TYPE 788  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     91    2
  17P GAIN WILD-TYPE  788   19
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               91                788
  1                2                 19
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    99   5
  17P GAIN WILD-TYPE 952   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     99    5
  17P GAIN WILD-TYPE  952    6
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               99                952
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P GAIN MUTATED                            0                            81
  17P GAIN WILD-TYPE                          1                           682
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P GAIN MUTATED                               10                   1
  17P GAIN WILD-TYPE                            182                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P GAIN MUTATED                       0                                1
  17P GAIN WILD-TYPE                     4                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17P GAIN MUTATED                    3              8
  17P GAIN WILD-TYPE                 14             40
D30V8, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  81                682
  INFILTRATING LOBULAR CARCINOMA                 10                182
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                  8                 40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    38  66
  17P GAIN WILD-TYPE 250 708
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     38   66
  17P GAIN WILD-TYPE  250  708
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                38                250
  YES               66                708
[1] 2 2
[1] FALSE
D30V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     7
  17P GAIN WILD-TYPE                                1    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          18    70
  17P GAIN WILD-TYPE                       152   666
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      18                152
  WHITE                                          70                666
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  83
  17P GAIN WILD-TYPE  34 775
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   83
  17P GAIN WILD-TYPE   34  775
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO               83                775
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   178  32
  17Q GAIN WILD-TYPE 738  96
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               210                834 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                 96 
$`17Q GAIN MUTATED`
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CU 
       11.44         9.96        47.24        13.68       121.94         5.19 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       56.81        33.76        25.22        35.05        34.29        31.82 
TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 
       49.84        20.75        23.77        60.72        20.25        52.47 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A7-A0CD 
       18.15       105.34        29.98        47.31        50.37        38.30 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       35.67        29.79        25.15        23.80        20.61        22.32 
TCGA-A7-A3J0 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06Z 
       10.29        14.93        17.92        13.02        29.03         1.02 
TCGA-A8-A07G TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       18.97        10.98         9.99        33.01        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       31.00        33.01        30.97        12.00         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H 
       49.05        33.07         8.98        14.01        10.85         5.72 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A04A 
       26.04        33.04         8.22        20.19         0.23         2.96 
TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A0J5 
        6.44         0.33         0.33        80.28        95.70        26.04 
TCGA-AO-A0J7 TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AQ-A1H3 
       20.32       102.58        98.27        57.30        61.87        32.52 
TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AW 
       32.91        73.64        83.87        51.25        61.28        63.62 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V 
      160.90        50.89        94.22         2.76        87.22        85.35 
TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0WV 
       79.00        73.18        58.92        54.21        66.15        79.63 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
      186.48        43.59        73.51        85.35        74.99        24.53 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 
       20.45        28.50        39.16        45.57        49.05        41.75 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A18L 
       42.90        31.17        15.65        36.85        51.32        26.66 
TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       37.74        66.05        51.39        55.69        49.58        25.81 
TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      114.15       122.89        63.35        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 
      130.16        18.64        12.66         3.16         1.87         4.08 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A27A TCGA-C8-A3M8 
       11.34        11.28         2.30         3.25        12.20         0.23 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ 
       13.97        14.17        18.71        12.03        12.03        20.09 
TCGA-D8-A1JT TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM 
       13.32        16.73        18.15        15.22        19.92        17.69 
TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y2 TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A107 
       16.31        16.54        14.24        10.09        12.26        34.42 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A15A 
       46.59        40.11        44.68        33.30        32.02        23.34 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       14.99        53.03        32.35        38.30        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 
       28.44        24.59         8.75         8.28        26.56        12.00 
TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       35.24        11.90        34.95         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B 
       21.21        34.65        34.59        35.64        34.13        22.75 
TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP 
       12.89        27.22        29.72        23.84        13.81        14.40 
TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 
       13.25        15.68        29.95        29.85        52.96        23.11 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DK 
        6.15        13.94        52.73        10.16        83.34        86.96 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-MS-A51U 
       69.30         2.60        15.32        14.70        12.36        22.39 
TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A6VO TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 
       22.32        41.92        28.21        13.12        16.93        15.39 

$`17Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       31.79         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        78.41        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       98.99       107.93        67.33        34.55        61.58       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       50.47        21.90        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       48.46        31.73        23.47        17.36        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25F 
       19.56        16.47       107.70        42.44        17.19        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        33.93        83.01        32.75        49.48 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       30.61        37.45        33.11        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3IY 
       29.56        31.36        24.26        23.74        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB 
       10.59        11.28        13.41        14.70        11.97        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       17.98        53.06        31.00        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       32.05         9.99         8.98         7.99        24.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       28.96        12.00         9.99        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       43.00        40.01        33.01        17.95        41.98         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        45.07        29.98         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.37         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       36.99        38.79        50.70         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OQ 
       18.67        13.58        12.26         1.68         0.03         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         0.33         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        52.18        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        50.24        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
      108.72       106.78       108.03        90.58        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        2.56        19.20       111.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       42.35        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      101.95       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M 
       17.23        37.81        76.21        62.14        33.73        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       78.51        84.20       104.28        97.84        76.01        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       50.96        83.77        89.00        78.48        72.76        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      143.21        20.25        62.86        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41        97.48       188.68        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.57       129.70        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      139.17       170.17        68.12       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        46.95        40.83        39.55        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       24.85        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 
       27.19        53.69        53.95        49.94        11.67        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       48.13        45.83        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        13.61        12.89        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P 
        2.01         7.23        20.12        90.84        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55         7.36        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 
      113.82        82.85        42.28        12.00        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       28.14        57.83        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28         8.94        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        0.39         2.24         1.12         1.05         4.11        12.33 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W 
       10.92         0.16        12.03        10.42         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.50         0.99         0.03        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
       19.46        11.90        20.88        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       21.14        19.20        14.17        17.49        16.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL 
       18.15        18.90        14.01        18.97        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        21.01        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        21.83        14.50        15.55        16.41        15.85 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        12.99        15.16        12.66        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.53        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
        8.02        12.10        43.00        27.52        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.17        43.33        34.26        31.96        28.60        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       25.41        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1AZ 
       11.05        13.02        19.56        17.06        14.07        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       53.62        33.01        28.50        16.47        17.10        37.41 
TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        39.62        19.66        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.87       106.75       102.61        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       15.72        30.61        34.92        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        13.48        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 
       12.59        35.77        25.84         9.86        28.27         2.56 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        32.09        40.24         1.12         6.58        21.27 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G 
       32.05        12.53        13.32        39.09        41.03        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.71        17.06         0.69         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       12.33        14.70         0.79        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
        8.48        18.21        18.90        16.57        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 
       22.82        40.41        41.13        39.78        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90        19.99        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL 
       79.10        75.02        70.85        72.10        85.15       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        11.44        10.95        25.05        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        7.46        14.50        14.73        14.07        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        42.77        26.04        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         9.93        16.50        16.80        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.23               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            186.48             234.28 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            26.610             23.675 
[1] "0.2 - 186.5 (26.6)" "0.0 - 234.3 (23.7)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED        16       14        1        1        77        47
  17Q GAIN WILD-TYPE      73       67        7        2       276       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1         32          8         11        4
  17Q GAIN WILD-TYPE         1        118         21         52       16
                    vv
clus                 STAGE TIS STAGE X
  17Q GAIN MUTATED           0       1
  17Q GAIN WILD-TYPE         1      12
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  16                 73
  STAGE IA                 14                 67
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA                77                276
  STAGE IIB                47                198
  STAGE III                 1                  1
  STAGE IIIA               32                118
  STAGE IIIB                8                 21
  STAGE IIIC               11                 52
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    49 131  22  11
  17Q GAIN WILD-TYPE 223 485 108  29
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               49                223
  T2              131                485
  T3               22                108
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    98  70  27  12
  17Q GAIN WILD-TYPE 403 280  90  63
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               98                403
  N1               70                280
  N2               27                 90
  N3               12                 63
[1] 4 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   183   4
  17Q GAIN WILD-TYPE 696  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    183    4
  17Q GAIN WILD-TYPE  696   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              183                696
  1                4                 17
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   206   7
  17Q GAIN WILD-TYPE 845   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    206    7
  17Q GAIN WILD-TYPE  845    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              206                845
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q GAIN MUTATED                            0                           167
  17Q GAIN WILD-TYPE                          1                           596
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q GAIN MUTATED                               24                   2
  17Q GAIN WILD-TYPE                            168                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q GAIN MUTATED                       0                                4
  17Q GAIN WILD-TYPE                     4                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17Q GAIN MUTATED                    5             11
  17Q GAIN WILD-TYPE                 12             37
D31V8, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 167                596
  INFILTRATING LOBULAR CARCINOMA                 24                168
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              5                 12
  OTHER  SPECIFY                                 11                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    70 143
  17Q GAIN WILD-TYPE 218 631
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     70  143
  17Q GAIN WILD-TYPE  218  631
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                70                218
  YES              143                631
[1] 2 2
[1] FALSE
D31V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0    12
  17Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          35   142
  17Q GAIN WILD-TYPE                       135   594
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      35                135
  WHITE                                         142                594
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 174
  17Q GAIN WILD-TYPE  32 684
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  174
  17Q GAIN WILD-TYPE   32  684
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO              174                684
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED   153  19
  18P GAIN WILD-TYPE 763 109
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               172                872 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                109 
$`18P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
      129.14        42.81        31.79        19.20        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ 
       24.79        33.76       101.72        79.76         8.38        18.61 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A7-A0CD TCGA-A7-A0CJ 
       31.73        23.47        33.93        47.31        38.30        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV 
       35.67        31.73        20.19        14.50        21.17        10.29 
TCGA-A7-A6VW TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A086 
        9.37         1.02        17.03         9.01         8.98        13.02 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 
       28.96        12.00        31.00       112.08        43.00        33.01 
TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A9 TCGA-A8-A0AB 
       12.00        29.98         8.98         0.99        27.02        17.03 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03Y 
       38.53        33.04        17.42        13.58         1.68         0.33 
TCGA-AN-A04C TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AO-A03P TCGA-AO-A0J2 
        1.78         0.33         7.96         0.33        95.70        32.78 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS 
       55.33       102.58        90.58        48.36        61.87         0.53 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AQ 
       17.79         2.56        74.79        65.36        52.77        43.07 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LH 
       50.89       104.28        53.36        79.00        89.00        20.25 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ 
       77.62       143.38       129.57       112.37       126.12       140.88 
TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A401 
      211.56       162.05       131.21        97.48        43.59        85.35 
TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP 
       68.12        24.85        44.05        44.02        45.83        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
        2.56        38.47         4.41        46.19        24.49        31.00 
TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18T TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A208 
       23.05        37.74         7.36       114.15        72.07        57.83 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A1HG 
        9.63         5.26        11.93        11.77        12.66        11.34 
TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1JP 
       12.20        20.88        15.78        12.03        20.09        21.01 
TCGA-D8-A1JT TCGA-D8-A1XW TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27N TCGA-E2-A10B 
       13.32        12.66        14.24        13.05         4.80        37.51 
TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A15C TCGA-E2-A15D 
       40.96        33.30        31.96        25.41        22.82        17.29 
TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 
       18.21        13.02        22.19        11.08        27.42        39.62 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NF 
      106.75        16.93         8.28        13.48        12.00        35.24 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RH 
        9.86         2.56         6.12        32.09         1.12        34.59 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1J6 
       23.51         0.69         7.13        14.40        15.39        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-GI-A2C9 
       22.82        29.82        23.11        19.99        17.49       109.87 
TCGA-GM-A2DC TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR 
       83.34        69.30         2.60        14.47        14.79        16.08 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A6VO 
       15.68        14.70        14.73        58.52        23.47        28.21 
TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA12 
        8.91         9.93        13.12        15.35 

$`18P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      134.40        80.28       107.61        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       49.48        19.33        48.46        23.77        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        83.01        29.98        32.75        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.72        11.05        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       36.95         0.99        38.01        33.01        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00         0.99        33.01        40.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       50.04        49.05        45.07        33.07         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       21.04         0.99        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        26.04        50.70         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        13.71        18.67 
TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
       12.26         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        50.24        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       106.78       108.03        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       41.62        28.37        14.73        82.62        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       26.93       130.09         5.65        15.62        32.52        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       111.32        73.64         5.26        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86       107.24       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
      114.02        85.97        75.55        61.84        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       76.11        43.73        43.56        39.98        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22        96.89        78.51        84.20         2.76        87.22 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       97.84        76.01        85.35        50.96        83.77        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       73.18        72.76        58.92        93.83       143.21        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I5 
       20.38        54.74        16.04        20.45        10.59       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
       12.13       220.90        50.70        65.72       146.50       176.98 
TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH 
       18.77        84.59       110.14       110.93        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      100.70        89.46       157.41       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88       101.52        73.51       139.17       170.17 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       74.99       103.63        71.15        24.53        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       48.36        56.94        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        25.71        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        41.75        48.13        42.90        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        17.26         3.22 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        47.41        16.27        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        32.58        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05        51.39        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63        72.07       144.59        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FY 
       10.52       109.28         8.94        18.64        23.51         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       18.87        21.76         9.44        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        2.24         1.87         1.12         1.05         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
        2.30         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       11.90        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       20.12        19.40        20.38        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        12.99        15.16        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I 
        9.93        14.14        17.42        16.04        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
        9.44        16.41        13.48         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        18.51        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F 
       23.87        14.79        25.05        23.34        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.65         3.88        20.98        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90        18.87       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       12.85        34.82        32.88        36.82        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        12.59        35.77        25.84        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC 
       34.95         3.02         2.76        21.21        32.09        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        21.27        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       12.53        13.32        39.09        22.75        41.03        12.89 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
       20.71        17.06        27.22         1.94        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW 
       12.33        23.84        14.70         0.79        13.81        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       55.00        52.73        25.91        22.09        34.03        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
       23.51         7.40        59.57       216.76        79.10        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12        62.43        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 
       22.26         2.63         7.46        14.50        12.36        14.07 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91        22.39         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD 
       17.36        14.07        19.73        40.11        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z 
       86.96         0.16         0.26        16.50        16.93        16.80 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       15.39        13.84        14.96        13.84        13.94        17.03 
TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.33               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            211.56             234.28 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            23.470             24.625 
[1] "0.3 - 211.6 (23.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED        10       13        1        0        77        33
  18P GAIN WILD-TYPE      79       68        7        3       276       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           1         17          6          8        4
  18P GAIN WILD-TYPE         1        133         23         55       16
                    vv
clus                 STAGE TIS STAGE X
  18P GAIN MUTATED           0       3
  18P GAIN WILD-TYPE         1      10
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 13                 68
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                77                276
  STAGE IIB                33                212
  STAGE III                 1                  1
  STAGE IIIA               17                133
  STAGE IIIB                6                 23
  STAGE IIIC                8                 55
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    36 109  21   6
  18P GAIN WILD-TYPE 236 507 109  34
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               36                236
  T2              109                507
  T3               21                109
  T4                6                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    99  44  15  13
  18P GAIN WILD-TYPE 402 306 102  62
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               99                402
  N1               44                306
  N2               15                102
  N3               13                 62
[1] 4 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   148   4
  18P GAIN WILD-TYPE 731  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    148    4
  18P GAIN WILD-TYPE  731   17
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              148                731
  1                4                 17
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   172   2
  18P GAIN WILD-TYPE 879   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    172    2
  18P GAIN WILD-TYPE  879    9
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE              172                879
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P GAIN MUTATED                            0                           142
  18P GAIN WILD-TYPE                          1                           621
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P GAIN MUTATED                               14                   2
  18P GAIN WILD-TYPE                            178                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P GAIN MUTATED                       1                                5
  18P GAIN WILD-TYPE                     3                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18P GAIN MUTATED                    0              9
  18P GAIN WILD-TYPE                 17             39
D32V8, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 142                621
  INFILTRATING LOBULAR CARCINOMA                 14                178
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  9                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    52 122
  18P GAIN WILD-TYPE 236 652
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     52  122
  18P GAIN WILD-TYPE  236  652
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                52                236
  YES              122                652
[1] 2 2
[1] FALSE
D32V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     7
  18P GAIN WILD-TYPE                                1    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                          46   101
  18P GAIN WILD-TYPE                       124   635
D32V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      46                124
  WHITE                                         101                635
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3 138
  18P GAIN WILD-TYPE  35 720
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  138
  18P GAIN WILD-TYPE   35  720
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              138                720
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED   129  18
  18Q GAIN WILD-TYPE 787 110
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               147                897 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                110 
$`18Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
      129.14        42.81        31.79        19.20        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ 
       24.79        33.76       101.72        79.76         8.38        18.61 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        23.47       105.34        33.93        47.31        34.98 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A6VW TCGA-A8-A079 
       38.30        30.61        20.19        14.50         9.37         9.01 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08T 
       10.98         8.98        13.02        28.96        12.00       112.08 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A0A9 
       43.00        33.01        12.00        29.98         8.98        27.02 
TCGA-A8-A0AB TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AR 
       17.03        13.58         1.68         0.33         1.78         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AO-A03P 
        0.33         0.33         7.96         0.33        12.33        95.70 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS 
       55.33       102.58        90.58        48.36        61.87         0.53 
TCGA-AQ-A54N TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24Z 
        2.56        65.36        52.77        50.89       104.28        79.00 
TCGA-AR-A2LH TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ 
       20.25       143.38       129.57       112.37       126.12       140.88 
TCGA-B6-A0RO TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BL 
      162.05        97.48        43.59        85.35        68.12        44.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       41.75        44.02        45.83        15.65         2.56        38.47 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HB TCGA-BH-A0HY 
        4.41         9.63        46.19        24.49        26.50        50.79 
TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A208 
       23.05        26.66        37.74        55.63         7.36        57.83 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U 
       18.64         9.63         5.26        11.93        11.77        12.66 
TCGA-C8-A1HG TCGA-C8-A1HN TCGA-C8-A27A TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1JP 
       11.34         3.25        12.20        12.03        20.09        21.01 
TCGA-D8-A1JT TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-E2-A10B TCGA-E2-A14T TCGA-E2-A14X 
       13.32        14.24        13.05        37.51        33.30        31.96 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 
       22.82        17.29        18.21        22.19        11.08        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 
       39.62       106.75        16.93         8.28        13.48        12.00 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA 
       35.24         9.86        34.95         2.56         6.12        32.09 
TCGA-E9-A1RD TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A5UP 
        1.12        23.51         0.69         7.13        26.07        14.40 
TCGA-E9-A6HE TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB 
       15.39        28.77        22.82        29.82        23.11        19.99 
TCGA-GM-A2DC TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A66I 
       83.34        69.30         7.10        14.79        14.70        23.47 
TCGA-OL-A97C TCGA-S3-A6ZG TCGA-S3-AA10 
        8.91        13.12        15.39 

$`18Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      134.40        80.28       107.61        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       49.48        19.33        48.46        23.77        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        42.44        17.19        18.15        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       39.65        83.01        29.98        32.75        49.48        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05         9.99         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        18.05        15.06        36.95         0.99        38.01 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        33.01        40.01        30.97        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       45.07        33.07         1.02        25.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       17.42        18.67        12.26         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.16         6.44         5.65         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        50.24        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       106.78       108.03        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT 
       41.62        28.37        14.73        82.62        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      101.95        83.87       114.02        85.97        75.55        61.84 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        33.73       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       84.20         2.76        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       85.35        50.96        83.77        89.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        58.92        93.83       143.21        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       54.74        16.04        20.45        10.59        77.62       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
       12.13       220.90        50.70        65.72       146.50       176.98 
TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
       18.77        84.59       110.14       110.93       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      189.01       234.28        81.17        78.02       172.96       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT 
      140.48       100.70        89.46       131.21       157.41       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      139.17       170.17        74.99       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       45.57        49.94        11.67        49.05        48.13        42.90 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
       17.26         3.22        67.86        47.41        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30        44.81        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        51.32        27.25         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        90.84        72.56        30.28        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A8FY TCGA-BH-A8FZ 
       10.52       109.28         8.94        23.51         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       21.76         9.44        11.77        12.66        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         0.03         9.50         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       20.12        19.40        20.38        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
        6.35        12.99        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         9.93        14.14        17.42        16.04        13.45 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        32.02        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       25.05        23.34        20.71        21.63        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       17.06        14.07        14.99        60.53        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        20.98        54.18        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90        18.87       102.61         8.75        43.04         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.82        32.88        36.82        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R5 
       12.59        35.77        25.84        11.90        28.27         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        21.21        32.09        40.24        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       13.32        39.09        22.75        41.03        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       17.06        27.22         1.94        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70         0.79        13.81        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
        7.40       109.87        59.57       216.76        79.10        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        28.21        19.73        40.11        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       86.96         0.16         0.26         9.93        16.50        16.93 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       16.80        13.84        15.35        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       17.03         3.81        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.33               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            162.05             234.28 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             23.11              24.72 
[1] "0.3 - 162.1 (23.1)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         9        9        1        0        65        30
  18Q GAIN WILD-TYPE      80       72        7        3       288       215
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           1         15          4          9        4
  18Q GAIN WILD-TYPE         1        135         25         54       16
                    vv
clus                 STAGE TIS STAGE X
  18Q GAIN MUTATED           0       2
  18Q GAIN WILD-TYPE         1      11
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  9                 72
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                65                288
  STAGE IIB                30                215
  STAGE III                 1                  1
  STAGE IIIA               15                135
  STAGE IIIB                4                 25
  STAGE IIIC                9                 54
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    29  98  16   5
  18Q GAIN WILD-TYPE 243 518 114  35
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               29                243
  T2               98                518
  T3               16                114
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    80  42  12  13
  18Q GAIN WILD-TYPE 421 308 105  62
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               80                421
  N1               42                308
  N2               12                105
  N3               13                 62
[1] 4 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   132   4
  18Q GAIN WILD-TYPE 747  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    132    4
  18Q GAIN WILD-TYPE  747   17
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0              132                747
  1                4                 17
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED   147   2
  18Q GAIN WILD-TYPE 904   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    147    2
  18Q GAIN WILD-TYPE  904    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE              147                904
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q GAIN MUTATED                            0                           122
  18Q GAIN WILD-TYPE                          1                           641
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q GAIN MUTATED                               13                   1
  18Q GAIN WILD-TYPE                            179                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q GAIN MUTATED                       1                                5
  18Q GAIN WILD-TYPE                     3                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18Q GAIN MUTATED                    0              6
  18Q GAIN WILD-TYPE                 17             42
D33V8, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 122                641
  INFILTRATING LOBULAR CARCINOMA                 13                179
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  6                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    45 104
  18Q GAIN WILD-TYPE 243 670
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     45  104
  18Q GAIN WILD-TYPE  243  670
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                45                243
  YES              104                670
[1] 2 2
[1] FALSE
D33V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     8
  18Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                          33    92
  18Q GAIN WILD-TYPE                       137   644
D33V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      33                137
  WHITE                                          92                644
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3 116
  18Q GAIN WILD-TYPE  35 742
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3  116
  18Q GAIN WILD-TYPE   35  742
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              116                742
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED   166  20
  19P GAIN WILD-TYPE 750 108
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               186                858 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                108 
$`19P GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SF TCGA-A1-A0SK TCGA-A2-A04Q TCGA-A2-A0CT TCGA-A2-A0D0 
       11.44        48.10        31.79        78.41        75.25        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EY 
       34.55        33.76        79.76        35.05        34.29        63.29 
TCGA-A2-A0SX TCGA-A2-A0T6 TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XU TCGA-A2-A3Y0 
       50.43        18.90        18.61        19.20        29.98        38.37 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        38.30        35.31        30.61        33.11        29.79 
TCGA-A7-A26E TCGA-A7-A3J0 TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06X TCGA-A8-A07R 
       31.36        10.29        21.17        12.10        31.00         8.98 
TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E 
       38.01        43.00        17.95        12.00        12.00        49.05 
TCGA-A8-A09M TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO 
       33.07         0.99        27.02         2.37        10.85        50.70 
TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A04C 
       14.83        17.42        13.58        20.19         0.33         1.78 
TCGA-AN-A0AK TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XW 
        7.36         7.00         0.36         0.33         0.33         5.59 
TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 
       80.28        81.63        32.78        20.32        55.33       102.58 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KS TCGA-AQ-A54O 
      106.78        90.58        98.27        64.04         0.53        32.91 
TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24V 
       65.36        61.28        63.62        62.14        50.89        85.35 
TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       50.96        58.92        93.83        40.54        20.38        54.74 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      112.37       176.98       131.21        21.47       113.79       129.57 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BA 
       43.59        73.51        85.35        24.53        56.94        37.22 
TCGA-BH-A0BJ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DO 
       21.70        41.75        44.02        42.90        45.83        17.26 
TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q 
       46.19        30.35        36.85        90.84        37.74        55.63 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A208 TCGA-BH-A5IZ TCGA-BH-A6R9 
        7.36        51.16        91.99        57.83        18.64         5.26 
TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A275 TCGA-D8-A13Z 
       11.93        12.66         3.16         2.30         0.03        20.88 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JH 
       14.17        13.48        19.20        14.17        12.03        14.01 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A27N 
       20.09        20.38        17.79        21.83        12.99         4.80 
TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14R 
       10.09        12.53        12.26        37.51        47.15        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A15M 
       31.96        28.60        18.51        25.41        23.24        11.05 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A576 TCGA-E2-A9RU 
       33.70        22.19        28.90        18.87        34.29        12.85 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA 
       12.00        13.12        36.56        35.24         2.76        32.09 
TCGA-E9-A1RD TCGA-E9-A22E TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
        1.12        12.89        17.06         0.69         1.94         7.13 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 
        0.72        30.18        14.70         0.79        14.40        28.77 
TCGA-EW-A1P4 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DD 
       29.82        19.99        13.94        10.16       109.87        75.02 
TCGA-HN-A2NL TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y 
        2.60        13.28        14.70        14.79         2.63        15.68 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG 
       14.73        14.07        36.36         8.91         9.93        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-UU-A93S TCGA-W8-A86G 
       16.93        16.80        15.39        15.35         3.81        11.41 

$`19P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        18.02       121.94        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        75.55 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19        98.99       107.93        56.81        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40        80.28       107.61        74.40        72.00 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.90        21.67        49.48        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        83.01        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       21.90        34.29        35.47        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        23.61        29.56        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        17.92        14.73        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       17.98        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        32.05         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        28.96        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
      112.08        40.01        33.01        30.97        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        9.99         1.02        50.04        45.07        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        26.04        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27        32.45        16.31        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55        11.44        13.71 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ 
       18.67        12.26         1.68         8.22         0.03         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         1.71         9.96         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         6.44         5.65         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.28         7.04         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        0.33         5.33        61.35        66.77        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F 
       71.80        99.25       108.72       108.03        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        89.00        78.48        73.18        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      143.21        20.25        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        39.39        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       18.35       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      101.52       139.17       170.17        74.99        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        59.84        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.94        11.67        49.05        48.13        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       23.05         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       72.56        30.28        37.55        66.05        51.39        69.93 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        26.14        38.60        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28         8.94        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        9.63         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         0.39         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 
        0.36         0.43         8.28         9.67         9.53         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       12.20         0.99         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        11.90        13.25        20.58        13.97 
TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       18.90        12.03        18.97        20.09        20.12        19.40 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31         6.35        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.41        13.48         0.76        13.08        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        27.12        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       27.42        39.62        19.66        24.59        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.92        26.56        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        13.48        39.55        12.59        35.77        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        3.02        21.21        32.09        40.24        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        41.03        23.51        20.71 
TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       27.22        24.56        29.72         0.76        26.07        18.41 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72        12.33        23.84        13.81        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90         6.15        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        23.51         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF 
       11.84        11.57        21.24        13.22         7.10        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       14.47        22.26        16.08         7.46        14.50        14.70 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       12.36        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       42.77        26.04        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11        47.01        64.21        86.96         0.16         0.26 
TCGA-S3-A6ZF TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       16.50        13.84        14.96        13.84        13.94        17.03 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.03               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            176.98             234.28 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            21.765             24.690 
[1] "0.0 - 177.0 (21.8)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED        13       13        0        0        79        40
  19P GAIN WILD-TYPE      76       68        8        3       274       205
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         24          5         11        1
  19P GAIN WILD-TYPE         2        126         24         52       19
                    vv
clus                 STAGE TIS STAGE X
  19P GAIN MUTATED           0       0
  19P GAIN WILD-TYPE         1      13
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  13                 76
  STAGE IA                 13                 68
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                79                274
  STAGE IIB                40                205
  STAGE III                 0                  2
  STAGE IIIA               24                126
  STAGE IIIB                5                 24
  STAGE IIIC               11                 52
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of 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    37 120  24   7
  19P GAIN WILD-TYPE 235 496 106  33
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               37                235
  T2              120                496
  T3               24                106
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED   103  54  19  12
  19P GAIN WILD-TYPE 398 296  98  63
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0              103                398
  N1               54                296
  N2               19                 98
  N3               12                 63
[1] 4 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   162   1
  19P GAIN WILD-TYPE 717  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    162    1
  19P GAIN WILD-TYPE  717   20
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0              162                717
  1                1                 20
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   184   4
  19P GAIN WILD-TYPE 867   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    184    4
  19P GAIN WILD-TYPE  867    7
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE              184                867
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P GAIN MUTATED                            1                           139
  19P GAIN WILD-TYPE                          0                           624
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P GAIN MUTATED                               26                   2
  19P GAIN WILD-TYPE                            166                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P GAIN MUTATED                       2                                5
  19P GAIN WILD-TYPE                     2                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19P GAIN MUTATED                    2             11
  19P GAIN WILD-TYPE                 15             37
D34V8, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 139                624
  INFILTRATING LOBULAR CARCINOMA                 26                166
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 11                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    57 131
  19P GAIN WILD-TYPE 231 643
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     57  131
  19P GAIN WILD-TYPE  231  643
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                57                231
  YES              131                643
[1] 2 2
[1] FALSE
D34V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     8
  19P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                          35   133
  19P GAIN WILD-TYPE                       135   603
D34V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      35                135
  WHITE                                         133                603
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6 155
  19P GAIN WILD-TYPE  32 703
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  155
  19P GAIN WILD-TYPE   32  703
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO              155                703
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED   193  24
  19Q GAIN WILD-TYPE 723 104
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               217                827 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                104 
$`19Q GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A2-A04P TCGA-A2-A04Q 
       11.44        48.10        13.68        31.79        18.02        78.41 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
       75.25        67.33        33.76        25.22        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 
       34.29        24.72        63.29        50.43         8.38        49.84 
TCGA-A2-A0T6 TCGA-A2-A0YH TCGA-A2-A1G0 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3Y0 
       18.90        21.67        20.25        33.93        29.98        38.37 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D 
       21.14        38.30        30.61        33.11        29.79        31.73 
TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VX 
       31.36        21.73        10.29        14.50        21.17        10.42 
TCGA-A8-A06O TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A092 
       13.02        43.00         8.98        38.01        43.00        30.97 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A0A7 
       17.95        12.00        12.00        49.05        25.02         0.99 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y 
       27.02         2.37        10.85        50.70        14.83        17.42 
TCGA-AC-A6IW TCGA-AC-A8OS TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM 
       13.58         2.30         0.33         1.78         7.36         0.16 
TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XW TCGA-AO-A03O 
        7.00         0.36         0.33         0.33         5.59        81.63 
TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       32.78        20.32       106.78        90.58        98.27        64.04 
TCGA-AO-A12F TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ 
       48.36        70.39         0.53         2.56        32.91        73.64 
TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       98.93        65.36        61.28        63.62        62.14        50.89 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A256 
       85.35        50.96        79.00        89.00        58.92        93.83 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO 
       40.54        20.38        54.74       112.37       176.98       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KC 
      140.88       100.70       131.21       113.79       129.57        43.59 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B6 
       73.51        85.35        24.53        20.45        39.55        56.94 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD 
       37.22        24.85        21.70        44.05        44.02        45.83 
TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18L 
       17.26        46.19        30.35        36.85        90.84        26.66 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.74        55.63         7.36        51.16        69.93        91.99 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A208 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12V 
       12.00        55.69        57.83         5.26        11.93        12.66 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z 
       12.66         3.16        12.03         2.30         3.25         8.28 
TCGA-C8-A274 TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
        9.53         0.03        20.88        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JL 
       19.20        14.17        12.03        12.03        14.01        20.09 
TCGA-D8-A1JN TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW 
       20.38        14.70        17.79        21.83        12.99        12.66 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C 
        4.80        10.09        12.53        12.26        37.51        40.11 
TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       47.15        38.60        31.96        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1II TCGA-E2-A1IN 
       27.12        23.24        21.63        11.05        33.70        22.19 
TCGA-E2-A1LG TCGA-E2-A576 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RA 
       18.87        34.29        12.00        13.12         2.76        32.09 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A249 
        1.12        35.64        22.75        12.89         1.94         7.13 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP 
        0.72        30.18        15.72        14.70         0.79        14.40 
TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A423 
       28.77        29.82         7.86        13.94        19.96        10.16 
TCGA-GM-A2DD TCGA-HN-A2NL TCGA-LD-A7W6 TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y 
       75.02         2.60        13.28        14.79         2.63        15.68 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A97C 
       14.73        14.07        22.39        36.36        23.47         8.91 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 
        9.93        13.12        16.93        16.80        15.39        15.35 
TCGA-W8-A86G 
       11.41 

$`19Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
      104.81       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        75.55         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        56.81        34.55        61.58       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       80.28       107.61        74.40        72.00        31.82        61.94 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.13        20.52        17.46        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.90        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        83.01        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       21.90        35.31        34.29        35.47        37.45        35.67 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        23.61        29.56        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       23.80        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       18.05        15.06        36.95        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        33.01       112.08        40.01        33.01 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       41.98         9.99         9.99         1.02        50.04        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         5.72         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP 
       33.04         0.92         2.27        32.45        16.31        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       11.44        13.71        18.67        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        0.03        20.19         1.12         1.32         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL 
        0.33         0.62         2.96         1.71         9.96         6.51 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ 
        7.59         7.17         6.28         7.04         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.33        80.28        61.35        66.77 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       95.70        68.75        47.87        58.95        29.13        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        26.04        37.48        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      108.72       108.03        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62        61.87        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR 
        5.65        15.62        32.52        19.20       111.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       74.79        86.66        42.35        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      101.95        83.87       114.02        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AY 
       39.98        43.07        17.23        37.81        76.21        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
      104.28        87.22        97.84        76.01        53.36        83.77 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       78.48        73.18        72.76       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN 
       54.21        66.15        52.11        38.17        39.39        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       20.45        10.59        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
      220.90       129.57        50.70        65.72       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      126.12        84.59       110.93       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       18.35        21.47       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 
       58.88       101.52       139.17       170.17        74.99        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        59.84        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       40.83        39.16        48.36        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       18.21        25.71        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        48.13        42.90        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       22.13        13.91        48.23        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        13.61        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
        8.81         2.01         7.23        20.12        72.56        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       37.55        66.05        51.39       113.82        82.85        42.28 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       72.07        28.14        26.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       18.64        23.51         9.63         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        9.44        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         0.39         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.05         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       11.28         0.16        10.42         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        0.43         9.67         9.50        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.23        13.02        12.49        13.41        19.46        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.25        20.58        21.14        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       15.78        18.15        18.90        18.97        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 
       19.40        21.01        12.20        13.32        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       16.41        15.85        16.31         6.35        15.16        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.48         0.76        13.08        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18         8.02        12.10        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       46.59        40.41        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       32.78        33.73        28.44        22.65         3.88        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       26.56        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        3.02        21.21        32.09        40.24        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        34.59        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        41.03        23.51        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       27.22        24.56        29.72         0.76        26.07        18.41 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       12.33        23.84        13.81        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
       19.99         6.15        10.52        14.43        34.55        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       52.73        25.91        22.09        34.03        17.49        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24        13.22         7.10        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       14.47        22.26        16.08         7.46        14.50        14.70 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       12.36        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC 
       17.36        14.07        28.21        19.73        40.11        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA11 
       64.21        86.96         0.16         0.26        16.50        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB41 
       14.96        13.84        13.94        17.03         3.81        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.03               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            176.98             234.28 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.83              24.79 
[1] "0.0 - 177.0 (21.8)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED        18       14        2        0        93        44
  19Q GAIN WILD-TYPE      71       67        6        3       260       201
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0         28          8         10        1
  19Q GAIN WILD-TYPE         2        122         21         53       19
                    vv
clus                 STAGE TIS STAGE X
  19Q GAIN MUTATED           0       0
  19Q GAIN WILD-TYPE         1      13
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 14                 67
  STAGE IB                  2                  6
  STAGE II                  0                  3
  STAGE IIA                93                260
  STAGE IIB                44                201
  STAGE III                 0                  2
  STAGE IIIA               28                122
  STAGE IIIB                8                 21
  STAGE IIIC               10                 53
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of 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    49 135  27   9
  19Q GAIN WILD-TYPE 223 481 103  31
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               49                223
  T2              135                481
  T3               27                103
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED   121  67  20  11
  19Q GAIN WILD-TYPE 380 283  97  64
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0              121                380
  N1               67                283
  N2               20                 97
  N3               11                 64
[1] 4 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   197   1
  19Q GAIN WILD-TYPE 682  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    197    1
  19Q GAIN WILD-TYPE  682   20
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0              197                682
  1                1                 20
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   216   4
  19Q GAIN WILD-TYPE 835   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    216    4
  19Q GAIN WILD-TYPE  835    7
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE              216                835
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q GAIN MUTATED                            0                           168
  19Q GAIN WILD-TYPE                          1                           595
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q GAIN MUTATED                               30                   3
  19Q GAIN WILD-TYPE                            162                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q GAIN MUTATED                       2                                5
  19Q GAIN WILD-TYPE                     2                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19Q GAIN MUTATED                    2             10
  19Q GAIN WILD-TYPE                 15             38
D35V8, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 168                595
  INFILTRATING LOBULAR CARCINOMA                 30                162
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 10                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    64 156
  19Q GAIN WILD-TYPE 224 618
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     64  156
  19Q GAIN WILD-TYPE  224  618
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                64                224
  YES              156                618
[1] 2 2
[1] FALSE
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    12
  19Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          36   158
  19Q GAIN WILD-TYPE                       134   578
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      36                134
  WHITE                                         158                578
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     8 180
  19Q GAIN WILD-TYPE  30 678
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8  180
  19Q GAIN WILD-TYPE   30  678
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 30
  NOT HISPANIC OR LATINO              180                678
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   355  51
  20P GAIN WILD-TYPE 561  77
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               406                638 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                51                 77 
$`20P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
      129.14       131.67        14.37        48.10        14.27        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04X 
       13.68         7.96        39.32        19.20        18.02        55.43 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       99.12        24.79        75.55        75.25         5.19        98.99 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
       56.81        67.33        33.76        25.22        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       34.29        31.82        63.29        27.12        44.88        50.43 
TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
        8.38        20.75        25.28        21.90        21.67        18.61 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A3KC 
       23.77        17.36        60.72        20.25        19.20        20.88 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
       33.93        83.01        24.39        21.14        38.30        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E 
       37.45        35.67        33.11        29.79        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD 
       25.15        23.74        20.61        14.70        14.93        14.50 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U 
       14.73        10.29         9.37        13.02        17.98        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       26.01        17.03        53.98        10.98         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J 
        9.99        45.07        13.02        38.01        12.00        37.05 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       31.00         0.99        33.01        30.97        17.95        41.98 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H 
        8.98        12.00         0.99        27.02        10.85         5.72 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5XS TCGA-AC-A62V 
       99.35        26.04        33.04         2.27         1.55        11.44 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X 
       17.42        13.58         1.68        20.19         1.12         0.33 
TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FV 
        0.33         2.96         1.78         9.96         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L 
        0.36         0.33         0.33        12.33         0.30        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J4 
       61.35        66.77        81.63        95.70        29.13        52.18 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL 
       20.32        53.03        72.00        76.77        50.24        55.33 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       71.80       106.78        90.58        98.27        57.30        48.36 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A54O 
       82.62        61.87         0.53       130.09        15.62        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       19.20        73.64        86.66        42.35        98.93        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW 
       65.36        83.87        61.84        39.98        61.28        63.62 
TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W 
      160.90       104.28        87.22        97.84        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       79.00        89.00        73.18        72.76        58.92        93.83 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       54.21        66.15        54.74        77.62       143.38       149.59 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH 
      129.57        65.72       112.37       110.14       211.56       189.01 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI 
      162.05       131.21        79.63       113.79        43.59        73.51 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        74.99        68.12       103.63        24.53        20.45 
TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       40.83        56.94        37.22        25.71        24.85        44.05 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       48.69        45.57        49.94        49.05        41.75        44.02 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       45.83        23.44        48.23         4.41        14.30         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 
       46.19        31.00        24.43        30.35        23.08        41.00 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       26.50        20.38        36.85        27.25        50.79         5.59 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q 
       42.35        44.81        23.05        90.84        37.74        55.63 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV 
        7.36        51.39        69.93        91.99        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH 
       55.69        49.58        31.53        97.48        24.66        36.92 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A5IZ TCGA-BH-A5J0 
       72.07        26.14        38.60         6.44        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        9.63         5.26        11.93        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.16         2.24         1.87 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 
        4.08        11.28         2.30         8.28         9.53         9.50 
TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
        0.23        13.41        20.88        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        19.20        14.17        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP 
       18.90        12.03        12.03        14.01        18.97        21.01 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XS 
       13.32        18.58        18.15        15.22        19.92        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27W TCGA-D8-A73U TCGA-D8-A73X 
       14.43        16.41        13.48        12.26        16.18        12.10 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14V 
       37.51        40.11        44.68        40.96        33.30        34.26 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       31.96        18.51        25.41        27.12        23.24        19.43 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A1AZ 
       25.05        22.82        12.92         9.04        13.02        60.53 
TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO 
       53.62        17.10        33.73        33.70        22.19        20.98 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z 
       27.42        19.66       106.75       102.61         8.75         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 
       30.61        26.56        34.29        12.85        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ 
       13.12        12.59        35.77        35.24         9.86        11.90 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        2.56         6.12         3.02        32.09        32.09        40.24 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22B 
        6.58        21.27        34.59        34.13        13.32        22.75 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 
       41.03        12.89        27.22         1.94         7.13         0.72 
TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY 
       29.72        23.84        14.70         0.79        14.40         8.48 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 
       16.57        15.68        28.77        29.85        41.13        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FS 
       18.48        19.99         6.15        13.94        19.96        52.73 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U 
       83.34        75.02        72.10        69.30         2.60        21.24 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.10        11.44        15.32        14.70        22.26         2.63 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N 
        7.46        14.70        27.91        22.32        23.47        26.04 
TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 
        8.91        86.96         9.93        16.50        13.12        15.39 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-Z7-A8R6 
       13.94        17.03        11.41       107.05 

$`20P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SQ 
        8.52        43.43        47.24        31.79        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      101.98        36.13       136.73       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93       107.93        34.55        61.58       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       80.28       107.61        74.40        72.00        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       99.19        54.64        44.28        17.52        17.13        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        18.21        50.47 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       49.48        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
       18.15       105.34        10.59        39.65        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        26.96        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       35.47        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       13.41        11.97        13.74        21.17        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        11.05        10.42         8.75        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       53.06        31.00         1.02         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
        7.99        18.05        15.06        36.95         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X 
       33.01        19.96         9.99        31.00       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        33.01        12.00         9.99         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       33.07        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.37         1.48        38.53        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OR 
       13.71        18.67        12.26         8.22         0.03         1.32 
TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AK 
        2.30         0.23         0.33         0.62         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        0.33         5.33         5.59        68.75        47.87        58.95 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       32.78        21.40        26.04        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 
       50.70        50.86        21.37        26.24        62.04       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
       99.25       108.72       108.03        64.04        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 
       14.73        70.39        17.79        24.79        26.93         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY 
       32.52         2.56       111.32         5.26        74.79        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
      107.24       101.95       114.02        85.97        75.55        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       51.25        48.82        76.11        43.73        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        76.21        62.14        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       94.22        96.89        78.51        84.20         2.76        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       53.36        83.77        78.48       143.21        20.25        62.86 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       52.11        38.17        39.39        40.54        20.38        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
       20.45        10.59        12.13       220.90        50.70       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
       68.45       234.28        81.17        78.02       172.96       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A40C 
       68.94        58.88       101.52       139.17       170.17        71.15 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        25.55        28.50        46.95        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ 
       48.36        56.98        51.68        32.02        18.21        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW 
       61.68        35.67        27.19        53.69        53.95        11.67 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       48.13        42.90        31.17        38.01        22.13        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       47.41        16.27        15.68        44.81        32.58        24.49 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA 
       10.78        15.16        37.78        35.51        24.56        52.96 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 
        5.85         2.50        13.61        12.89        51.32        23.93 
TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       24.95         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ES 
       72.56        30.28        37.55        66.05        51.16       113.82 
TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
       82.85        17.69        25.81        89.16       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17        74.73       122.89        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
      144.59        72.07        28.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FY 
       10.65        20.12        10.52       109.28         8.94         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12Z TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        0.39         1.12         1.05         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34         0.16        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A 
        0.23         0.36         0.43         9.67         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.99         0.03        13.02        12.49        19.46        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JJ TCGA-D8-A1JK 
       13.25        20.58        17.49        16.50        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 
       20.09        19.40        20.38        12.20        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.83        14.50        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.85         6.35        15.16        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P 
       16.04        13.45        13.05         9.44         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.53        33.37        18.51        21.67 
TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        8.02        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.44        28.87        47.15        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       43.33        32.02        28.60        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       23.34        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       19.40        20.58        11.05        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        39.62        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A573 
       18.87        43.04        16.93         5.52        15.72        34.92 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NG 
       34.82        32.88        36.82        36.56        39.55        25.84 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE 
       28.27        34.95         2.76        21.21         1.12        34.65 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H 
       35.64        32.05        12.53        39.09        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       17.06         0.69        24.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       30.18        15.72        12.33        13.81        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW 
       39.72        18.21        18.90        13.25        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 
       29.95        40.41        39.78        52.96        29.82        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
        7.86        18.90        10.52        14.43        34.55        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF 
        7.40       109.87        59.57       216.76        79.10        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        62.43        11.84        11.57        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO 
       10.62        24.95        10.95        25.05        17.06        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79        16.08        15.68        14.50        12.36        14.73 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.07        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       20.38        26.70        65.62        41.92        42.77        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        28.21        19.73        40.11        47.01        64.21 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.16         0.26        16.93        16.80        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       14.96        13.84         3.81        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.23               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            211.56             234.28 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             24.48              24.56 
[1] "0.2 - 211.6 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED        37       27        1        1       143        87
  20P GAIN WILD-TYPE      52       54        7        2       210       158
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           1         65         13         19       10
  20P GAIN WILD-TYPE         1         85         16         44       10
                    vv
clus                 STAGE TIS STAGE X
  20P GAIN MUTATED           1       3
  20P GAIN WILD-TYPE         0      10
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  37                 52
  STAGE IA                 27                 54
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA               143                210
  STAGE IIB                87                158
  STAGE III                 1                  1
  STAGE IIIA               65                 85
  STAGE IIIB               13                 16
  STAGE IIIC               19                 44
  STAGE IV                 10                 10
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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   101 247  42  18
  20P GAIN WILD-TYPE 171 369  88  22
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1              101                171
  T2              247                369
  T3               42                 88
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED   195 125  60  23
  20P GAIN WILD-TYPE 306 225  57  52
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              195                306
  N1              125                225
  N2               60                 57
  N3               23                 52
[1] 4 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   355  10
  20P GAIN WILD-TYPE 524  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    355   10
  20P GAIN WILD-TYPE  524   11
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              355                524
  1               10                 11
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   403   8
  20P GAIN WILD-TYPE 648   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    403    8
  20P GAIN WILD-TYPE  648    3
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              403                648
  MALE                  8                  3
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P GAIN MUTATED                            0                           335
  20P GAIN WILD-TYPE                          1                           428
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P GAIN MUTATED                               44                   2
  20P GAIN WILD-TYPE                            148                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P GAIN MUTATED                       2                               10
  20P GAIN WILD-TYPE                     2                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20P GAIN MUTATED                    1             16
  20P GAIN WILD-TYPE                 16             32
D36V8, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 335                428
  INFILTRATING LOBULAR CARCINOMA                 44                148
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 16                 32
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   131 280
  20P GAIN WILD-TYPE 157 494
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    131  280
  20P GAIN WILD-TYPE  157  494
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               131                157
  YES              280                494
[1] 2 2
[1] FALSE
D36V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0    22
  20P GAIN WILD-TYPE                                1    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          71   278
  20P GAIN WILD-TYPE                        99   458
D36V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      71                 99
  WHITE                                         278                458
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11 333
  20P GAIN WILD-TYPE  27 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11  333
  20P GAIN WILD-TYPE   27  525
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 27
  NOT HISPANIC OR LATINO              333                525
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   385  55
  20Q GAIN WILD-TYPE 531  73
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               440                604 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                55                 73 
$`20Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG 
      129.14       131.67         9.96        14.37        48.10        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04W 
       20.88        13.68         7.96        19.20        18.02       101.98 
TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       55.43        99.12        24.79        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ 
       98.99        56.81        67.33        33.76        25.22        79.76 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0SX 
       35.05        34.29        31.82        63.29        44.88        50.43 
TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
       20.75        25.28        18.21        21.90        21.67        18.61 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B 
       23.77        17.36        60.72        20.25        19.20        42.44 
TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A4RX 
      105.34        20.88        33.93        83.01        47.31        24.39 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        38.30        30.61        37.45        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A425 
       31.73        20.19        25.15        23.74        20.61        14.70 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV 
       14.93        14.50        21.17        17.92        14.73        10.29 
TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       13.02        17.98        29.03        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.01        10.98         8.98        24.99         9.99        45.07 
TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P 
       13.02        38.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        33.01        43.00        30.97        17.95        41.98 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23G 
        1.02         8.98        12.00         0.99        27.02        10.85 
TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 
        5.72        99.35        26.04        33.04         2.27        16.57 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP 
        1.55        11.44        17.42        13.58         1.68        20.19 
TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM 
        1.12         0.33         0.33         1.78         9.96         0.16 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.36         0.33         0.33         0.33        12.33         0.30 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03V 
       80.28        61.35        66.77        81.63        47.87        29.13 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL 
       20.32        53.03        72.00        76.77        50.24        55.33 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       71.80       106.78        90.58        98.27        57.30        48.36 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       82.62        61.87        17.79        24.79       130.09        15.62 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       19.20        73.64        86.66        42.35        98.93        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AV 
      107.24        83.87        61.84        51.25        39.98        61.28 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       63.62       160.90        94.22       104.28        87.22        97.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
       85.35        50.96        79.00        89.00        73.18        58.92 
TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I1 
       93.83        54.21        66.15        20.38        54.74        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH 
      143.38       149.59        12.13       129.57        65.72       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RU 
      176.98       110.14       211.56        81.17       162.05       131.21 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       79.63       113.79        43.59       101.52        73.51       139.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        74.99        68.12       103.63        24.53        20.45 
TCGA-BH-A0AY TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP 
       25.55        56.94        37.22        25.71        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD 
       45.57        49.94        49.05        41.75        44.02        45.83 
TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E9 
       23.44        48.23         3.22         4.41        14.30        46.19 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB 
       31.00        24.43        30.35        23.08        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 
       20.38        36.85        27.25        50.79         5.59        42.35 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T 
       44.81        90.84        26.66        37.74        55.63         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93        91.99        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FM 
       49.58        31.53        97.48        24.66        36.92        45.63 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28Q TCGA-BH-A5IZ 
       72.07        26.14        38.60        57.83         6.44        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P 
       23.51         9.63         5.26        11.93        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN 
        1.87         4.08        11.34        11.28         2.30         3.25 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HR 
        8.28         9.53         9.50        12.20         0.23        13.41 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        14.17        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1JT 
       12.03        12.03        14.01        18.97        21.01        13.32 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XQ 
       18.58        27.58        18.15        15.22        19.92        16.41 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31        12.99        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
        9.93        14.43        16.41        13.48        10.09        12.26 
TCGA-D8-A73X TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R 
       12.10        37.51        40.11        44.68        40.96        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A152 
       33.17        33.30        34.26        31.96        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H 
       23.24        19.43        25.05        23.34        22.82        12.92 
TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 
        9.04        11.05        13.02        17.06        60.53        53.62 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 
       17.10        33.73        33.70        22.19        20.98        27.42 
TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 
       19.66       106.75       102.61         8.75         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        26.56        34.29        12.85        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 
       12.00        13.12        35.77         9.86        11.90        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         6.12         3.02         2.76        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 
       40.24        34.65         6.58        21.27        34.59        34.13 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 
       13.32        22.75        41.03        12.89         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK 
        1.94         7.13         0.72        29.72        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        0.79        14.40         8.48        16.57        15.68        28.77 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB 
       29.85        40.41        41.13        23.11        18.48        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DC 
        6.15        13.94        52.73        10.16         7.40        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       75.02        70.85        85.15        69.30         2.60        11.84 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       21.24         7.10        11.44        15.32        14.70        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5RZ 
        2.63        15.68        14.70        12.36        27.91        22.32 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LX 
       23.47        26.04         8.91        47.01        86.96         0.16 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA17 TCGA-UL-AAZ6 
        9.93        16.50        13.12        15.39        13.94        17.03 
TCGA-W8-A86G TCGA-Z7-A8R6 
       11.41       107.05 

$`20Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       43.43        47.24        31.79        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       36.13       136.73       114.81        92.48        88.60       107.93 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
      107.93        34.55        61.58       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
      107.61        74.40        72.00        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        27.12        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YF 
       49.84        20.52        17.46        18.90        32.55        50.47 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       49.48        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       10.59        39.65        29.98        32.75        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        38.37         7.30        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A13G 
       21.90        35.31        34.29        35.47        35.67        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       29.56        31.36        24.26        23.80        21.73        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       11.34        10.59        10.29        11.28        13.41        11.97 
TCGA-A7-A4SB TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX 
       13.74        12.10        10.72        11.05         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z 
        8.75        13.02         1.02        53.06        31.00         1.02 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       32.05         9.99         7.99        18.05        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T 
        0.99        28.96        33.01         9.99        31.00       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        33.01        12.00         9.99         9.99        12.00 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 
       25.02        19.04        15.02         0.99        14.01        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        17.03        38.04         0.95         2.37 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.53        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62X TCGA-AC-A6IV 
       14.99        19.79        23.24        24.79        13.71        18.67 
TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A041 
       12.26         8.22         0.03         1.32         2.30         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.62         2.96         1.71         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 
        5.33         5.59        95.70        68.75        58.95        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       21.40        52.18        26.04        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 
       50.70        50.86        21.37        26.24        62.04       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
       99.25       108.72       108.03        64.04        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 
       14.73        70.39         0.53        26.93         5.65        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY 
        2.56        32.91       111.32         5.26        74.79        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       101.95       114.02        85.97        75.55        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR 
       48.82        76.11        43.73        43.56        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M 
       37.81        76.21        62.14        33.73        50.89        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
       78.51        84.20         2.76        76.01        53.36        83.77 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       78.48        72.76       143.21        20.25        62.86        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        16.04        20.45        10.59 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      220.90        50.70       146.50        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      110.93       140.88        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A2IU TCGA-B6-A40C 
      186.48        28.27        68.94        58.88       170.17        71.15 
TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       48.36        56.98        51.68        32.02        18.21        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       21.70        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       11.67        48.13        42.90        31.17        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        17.26        15.65         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       47.41        16.27        15.68         9.63        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW 
       52.96         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       23.93        24.95        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V 
       20.12        72.56        30.28        37.55        66.05        51.16 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB 
      113.82        82.85        17.69        25.81        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        33.17        74.73       122.89        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
      144.59        72.07        28.14        83.31       130.16        10.65 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.12        10.52       109.28         8.94         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A12Z 
       21.76         9.44        11.77        11.77        12.66         0.39 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ 
        1.12         1.05         4.11        12.33        10.92         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.03        10.42         0.30         0.23         0.36         0.43 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.67         0.03         0.99         0.03        13.02        12.49 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JJ 
       19.46        11.90        20.58        17.49        16.50        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU 
       20.12        20.09        19.40        20.38        12.20        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        16.73        25.74        23.90        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        21.83        14.50        17.69        15.55        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
        6.35        15.16        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       13.45        13.05         9.44         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18         8.02 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E 
       43.00        34.42        27.52        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       28.87        47.15        38.24        43.33        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15E 
       18.51        21.04        23.87        14.79        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P 
       21.63        18.21        17.42        19.40        20.58        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.07        14.99        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       16.47        38.30        37.41        32.78        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        11.08        54.18        39.62        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90        18.87        43.04        16.93         5.52        15.72 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       34.82        32.88        36.56        39.55        12.59        35.24 
TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 
       25.84        28.27        21.21         1.12        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A24A 
       12.53        39.09        23.51        20.71        17.06        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       13.81        15.39        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 
       13.25        25.94        22.82        29.95        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF 
       29.82        30.08         7.86        18.90        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        23.51       109.87        59.57       216.76        79.10 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       18.12        62.43        11.57        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP 
       24.95        10.95        25.05        17.06        14.47        14.79 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
       16.08         7.46        14.50        14.73        14.07        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DD TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z 
       19.73        40.11        64.21         0.26        16.93        16.80 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-WT-AB41 
       13.84        15.35        14.96        13.84         3.81        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       29.03        15.35        16.04       108.07 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.16               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            211.56             234.28 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             24.48              24.56 
[1] "0.2 - 211.6 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED        36       29        1        1       154        98
  20Q GAIN WILD-TYPE      53       52        7        2       199       147
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           1         70         15         24        9
  20Q GAIN WILD-TYPE         1         80         14         39       11
                    vv
clus                 STAGE TIS STAGE X
  20Q GAIN MUTATED           1       3
  20Q GAIN WILD-TYPE         0      10
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  36                 53
  STAGE IA                 29                 52
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA               154                199
  STAGE IIB                98                147
  STAGE III                 1                  1
  STAGE IIIA               70                 80
  STAGE IIIB               15                 14
  STAGE IIIC               24                 39
  STAGE IV                  9                 11
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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   102 274  44  22
  20Q GAIN WILD-TYPE 170 342  86  18
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              102                170
  T2              274                342
  T3               44                 86
  T4               22                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   206 139  63  28
  20Q GAIN WILD-TYPE 295 211  54  47
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              206                295
  N1              139                211
  N2               63                 54
  N3               28                 47
[1] 4 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   383  10
  20Q GAIN WILD-TYPE 496  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    383   10
  20Q GAIN WILD-TYPE  496   11
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              383                496
  1               10                 11
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   438   7
  20Q GAIN WILD-TYPE 613   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    438    7
  20Q GAIN WILD-TYPE  613    4
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              438                613
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q GAIN MUTATED                            0                           364
  20Q GAIN WILD-TYPE                          1                           399
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q GAIN MUTATED                               48                   1
  20Q GAIN WILD-TYPE                            144                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q GAIN MUTATED                       2                               10
  20Q GAIN WILD-TYPE                     2                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20Q GAIN MUTATED                    1             19
  20Q GAIN WILD-TYPE                 16             29
D37V8, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 364                399
  INFILTRATING LOBULAR CARCINOMA                 48                144
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 19                 29
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   135 310
  20Q GAIN WILD-TYPE 153 464
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    135  310
  20Q GAIN WILD-TYPE  153  464
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               135                153
  YES              310                464
[1] 2 2
[1] FALSE
D37V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0    26
  20Q GAIN WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          79   296
  20Q GAIN WILD-TYPE                        91   440
D37V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          26                 34
  BLACK OR AFRICAN AMERICAN                      79                 91
  WHITE                                         296                440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11 363
  20Q GAIN WILD-TYPE  27 495
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11  363
  20Q GAIN WILD-TYPE   27  495
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 27
  NOT HISPANIC OR LATINO              363                495
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   161  33
  21Q GAIN WILD-TYPE 755  95
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               194                850 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                33                 95 
$`21Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04U 
      129.14        20.88        13.68        28.01        18.02        87.25 
TCGA-A2-A0CM TCGA-A2-A0CU TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       24.79         5.19        79.76        63.29        99.19        27.12 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YM 
       17.13         8.38        49.84        18.21        21.90        31.73 
TCGA-A2-A1G1 TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4S1 
       19.20        39.65        29.98        49.48        47.31        26.96 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26H 
       35.67        29.79        31.73        20.19        25.15        23.80 
TCGA-A7-A26I TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q 
       21.73        13.74        21.17        10.29        13.02         1.02 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       26.01        17.03        53.98         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A091 
       45.07        38.01         9.99        31.00        43.00        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0AB 
       30.97        17.95        29.98         1.02        14.01        17.03 
TCGA-AC-A23G TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW 
       10.85        26.04        33.04         2.27        17.42        13.58 
TCGA-AN-A03Y TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         7.04         0.33        66.77        81.63 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KT TCGA-AQ-A54O 
       71.80       106.78        98.27        64.04        17.79        32.91 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AR TCGA-AR-A1AV 
       98.93        55.86        65.36        52.77        17.23        61.28 
TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A2LR 
       62.14        50.89        87.22        79.00        78.48        20.38 
TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
       54.74        77.62       112.37        18.77        84.59       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KF 
      140.88       211.56       162.05       131.21       113.79       101.52 
TCGA-B6-A1KI TCGA-B6-A402 TCGA-BH-A0AY TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BR 
       73.51        74.99        25.55        56.98        44.05        53.69 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EB 
       45.57        49.05        44.02         2.56         9.63        24.49 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18Q TCGA-BH-A1EN TCGA-BH-A1EV 
       31.00        30.35        36.85        55.63        69.93        12.00 
TCGA-BH-A1EX TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A5IZ 
       49.58       114.15        72.07        26.14        38.60        18.64 
TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 
       11.77         0.39         3.16         2.24         1.87         1.05 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-D8-A13Y TCGA-D8-A13Z 
        2.30         0.43         0.03         9.50        11.90        20.88 
TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1XD TCGA-D8-A1XJ 
       19.20        12.03        14.01        20.12        17.16        21.83 
TCGA-D8-A1XK TCGA-D8-A1XU TCGA-D8-A1XW TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14P 
       14.50        12.99        12.66        37.51        44.68        40.96 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15M 
       38.60        31.96        18.51        19.43        25.05        11.05 
TCGA-E2-A15O TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1IN TCGA-E2-A1L9 TCGA-E2-A1LE 
       13.02        60.53        53.62        22.19        19.66        28.90 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1R7 TCGA-E9-A1RD 
        8.75        16.93        34.92        12.85        21.21         1.12 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A3X8 
       34.65        34.59        41.03         0.69        29.72        15.72 
TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC 
       14.40        40.41        29.82        23.11         7.86         6.15 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DF 
       19.96        55.00        25.91        10.16        83.34        70.85 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z 
        7.10        11.44        14.47        14.79        15.68         7.46 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-S3-AA0Z TCGA-S3-AA10 
       12.36        14.73        36.36        20.38        16.80        15.39 
TCGA-UL-AAZ6 TCGA-W8-A86G 
       17.03        11.41 

$`21Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      104.81        78.41       121.94        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55        75.25        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40        80.28       107.61        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU 
       35.05        34.29        31.82        61.94        24.72        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.88        50.43        44.28        17.52        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       10.59        20.88        33.93        83.01        32.75        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       30.61        37.45        33.11        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       29.03        31.00         1.02         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       10.98         7.99        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       31.00         0.99        33.01       112.08        40.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       49.05        45.07        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
        0.99        27.02        38.04         0.95         2.37         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55        11.44        13.71        18.67        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.17         6.28         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 
       21.37        26.24        50.24        62.04        55.33       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12F 
       99.25       108.72       108.03        90.58        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U1 
       74.79        86.66        42.35        64.83       107.24       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK 
       83.87       114.02        85.97        75.55        61.84        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       37.81        76.21        63.62        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       96.89        78.51        84.20         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
       76.01        53.36        85.35        50.96        83.77        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 
       40.54        16.04        20.45        10.59       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      176.98       126.12       110.93        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       58.88        43.59       139.17       170.17        85.35        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ 
      103.63        71.15        24.53        59.84        20.45        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       46.95        40.83        39.55        39.16        48.36        56.94 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS 
       21.70        61.68        35.67        48.69        27.19        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        41.75        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       28.14        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28         8.94        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66        12.66         1.12         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.53        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.49        13.41        19.46        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       18.71        15.78        18.15        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        27.58        18.15        12.39        15.22        14.73 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        15.16        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       47.15        38.24        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 
       32.02        28.60        25.41        27.12        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 
       20.58        19.56        17.06        14.07        14.99        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
        3.88        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       24.59        40.47        18.87       106.75       102.61        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         8.28        30.61        26.56        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF 
        3.02         2.76        32.09        32.09        40.24         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        20.71        17.06 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       27.22         1.94         7.13        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41        30.18        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        13.81        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       52.96        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        14.43        34.55        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        75.02        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       62.43        11.84        11.57        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       10.62        24.95        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A7SZ 
       14.70        22.26         2.63        16.08        14.50        14.70 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       14.07        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        16.50        13.12        16.93        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-WT-AB41 TCGA-WT-AB44 
       14.96        13.84        13.94         3.81        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.03               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            211.56             234.28 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.02              24.41 
[1] "0.0 - 211.6 (25.0)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.6"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        12       12        1        1        71        39
  21Q GAIN WILD-TYPE      77       69        7        2       282       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0         31          3         16        4
  21Q GAIN WILD-TYPE         2        119         26         47       16
                    vv
clus                 STAGE TIS STAGE X
  21Q GAIN MUTATED           0       3
  21Q GAIN WILD-TYPE         1      10
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  12                 77
  STAGE IA                 12                 69
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA                71                282
  STAGE IIB                39                206
  STAGE III                 0                  2
  STAGE IIIA               31                119
  STAGE IIIB                3                 26
  STAGE IIIC               16                 47
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    45 121  22   5
  21Q GAIN WILD-TYPE 227 495 108  35
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               45                227
  T2              121                495
  T3               22                108
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    85  66  21  17
  21Q GAIN WILD-TYPE 416 284  96  58
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               85                416
  N1               66                284
  N2               21                 96
  N3               17                 58
[1] 4 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   168   4
  21Q GAIN WILD-TYPE 711  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    168    4
  21Q GAIN WILD-TYPE  711   17
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0              168                711
  1                4                 17
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   193   2
  21Q GAIN WILD-TYPE 858   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    193    2
  21Q GAIN WILD-TYPE  858    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE              193                858
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q GAIN MUTATED                            0                           167
  21Q GAIN WILD-TYPE                          1                           596
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q GAIN MUTATED                               16                   2
  21Q GAIN WILD-TYPE                            176                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q GAIN MUTATED                       0                                0
  21Q GAIN WILD-TYPE                     4                               30
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  21Q GAIN MUTATED                    1              9
  21Q GAIN WILD-TYPE                 16             39
D38V8, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 167                596
  INFILTRATING LOBULAR CARCINOMA                 16                176
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 30
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  9                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    65 130
  21Q GAIN WILD-TYPE 223 644
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     65  130
  21Q GAIN WILD-TYPE  223  644
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                65                223
  YES              130                644
[1] 2 2
[1] FALSE
D38V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1    10
  21Q GAIN WILD-TYPE                                0    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                          41   120
  21Q GAIN WILD-TYPE                       129   616
D38V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          10                 50
  BLACK OR AFRICAN AMERICAN                      41                129
  WHITE                                         120                616
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9 151
  21Q GAIN WILD-TYPE  29 707
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9  151
  21Q GAIN WILD-TYPE   29  707
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 29
  NOT HISPANIC OR LATINO              151                707
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    82  14
  22Q GAIN WILD-TYPE 834 114
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                96                948 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                114 
$`22Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL 
        9.96        31.79        19.20        87.25       101.98        99.12 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0T1 TCGA-A2-A1FV TCGA-A2-A1G1 TCGA-A7-A0CD 
       56.81        33.76        17.13        23.47        19.20        38.30 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A079 
       29.79        25.15        10.29        10.42        13.02         9.01 
TCGA-A8-A08B TCGA-A8-A08R TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X 
       38.01         0.99        33.01        29.98        33.07        14.01 
TCGA-AC-A23H TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A0AL 
        5.72         2.27        16.57        11.44         1.12         6.51 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A12B 
        0.16         0.33         7.59         0.33         0.33        98.27 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TV 
       48.36        41.62       130.09         5.65       111.32        42.35 
TCGA-AR-A0U1 TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A2LR TCGA-B6-A0RS TCGA-B6-A0RU 
      101.95        53.36        85.35        20.38       100.70       131.21 
TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A402 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0DL 
       79.63        43.59        74.99        24.85        41.75        48.23 
TCGA-BH-A0E2 TCGA-BH-A0HY TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EV 
       14.30        50.79        55.63        51.39        69.93        12.00 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12O 
       72.07        26.14        38.60        57.83        11.93        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A1HG TCGA-D8-A142 TCGA-D8-A1JC 
       11.77        12.66         0.39        11.34        13.97        15.78 
TCGA-D8-A1JE TCGA-D8-A1JK TCGA-D8-A1XJ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27M 
       18.90        20.12        21.83        12.66        15.32        13.48 
TCGA-D8-A27W TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A1B0 TCGA-E9-A1NC TCGA-E9-A22B 
       12.26        31.96        27.12        53.62        39.55        22.75 
TCGA-E9-A243 TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2DF 
       17.06        14.40        40.41        23.51       109.87        70.85 
TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A8F5 
       69.30        15.32        14.79        16.08        14.70        14.73 

$`22Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO 
       63.12        55.43        36.13       136.73        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        67.33        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        17.36        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       11.05         9.37         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        28.96        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00        31.00        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       43.00        40.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       45.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       38.79        26.04        50.70        33.04         0.92        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
       16.31        14.83        22.19        14.99        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR 
       12.26         1.68         8.22         0.03        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AR 
        2.96         1.78         1.71         9.96         7.36         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         6.44         5.65         7.96         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        52.18        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       90.58        64.04        57.30        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       15.62        32.52         2.56        32.91        19.20        73.64 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        74.79        86.66        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24        65.36        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        63.62        62.14        33.73       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       87.22        97.84        76.01        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       89.00        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      143.21        20.25        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        18.35        21.47       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        24.53        59.84        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       46.95        40.83        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       90.84        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.66       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       72.07       144.59        28.14        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
        9.44        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         3.16         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.50        12.20         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        14.17        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       17.49        16.50        18.71        18.15        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       15.55        16.41        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       32.02        28.60        18.51        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        60.53        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.56        12.59        35.77        35.24        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       32.05        12.53        13.32        39.09        41.03        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       23.51        20.71         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        15.72        12.33        23.84        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       13.81        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       22.82        29.95        29.85        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        10.16         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       14.70        14.47        22.26         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        12.36        14.07        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       13.12        16.93        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.16               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            131.21             234.28 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            23.110             24.575 
[1] "0.2 - 131.2 (23.1)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         7        5        0        1        42        18
  22Q GAIN WILD-TYPE      82       76        8        2       311       227
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0         14          7          3        1
  22Q GAIN WILD-TYPE         2        136         22         60       19
                    vv
clus                 STAGE TIS STAGE X
  22Q GAIN MUTATED           0       0
  22Q GAIN WILD-TYPE         1      13
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   7                 82
  STAGE IA                  5                 76
  STAGE IB                  0                  8
  STAGE II                  1                  2
  STAGE IIA                42                311
  STAGE IIB                18                227
  STAGE III                 0                  2
  STAGE IIIA               14                136
  STAGE IIIB                7                 22
  STAGE IIIC                3                 60
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of 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    18  64   9   7
  22Q GAIN WILD-TYPE 254 552 121  33
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               18                254
  T2               64                552
  T3                9                121
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    53  27  10   4
  22Q GAIN WILD-TYPE 448 323 107  71
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               53                448
  N1               27                323
  N2               10                107
  N3                4                 71
[1] 4 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    85   1
  22Q GAIN WILD-TYPE 794  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     85    1
  22Q GAIN WILD-TYPE  794   20
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               85                794
  1                1                 20
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    97   1
  22Q GAIN WILD-TYPE 954  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     97    1
  22Q GAIN WILD-TYPE  954   10
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               97                954
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q GAIN MUTATED                            0                            80
  22Q GAIN WILD-TYPE                          1                           683
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q GAIN MUTATED                                4                   1
  22Q GAIN WILD-TYPE                            188                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q GAIN MUTATED                       0                                2
  22Q GAIN WILD-TYPE                     4                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  22Q GAIN MUTATED                    1             10
  22Q GAIN WILD-TYPE                 16             38
D39V8, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  80                683
  INFILTRATING LOBULAR CARCINOMA                  4                188
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 10                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    22  76
  22Q GAIN WILD-TYPE 266 698
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     22   76
  22Q GAIN WILD-TYPE  266  698
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                22                266
  YES               76                698
[1] 2 2
[1] FALSE
D39V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  1     7
  22Q GAIN WILD-TYPE                                0    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                          20    58
  22Q GAIN WILD-TYPE                       150   678
D39V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      20                150
  WHITE                                          58                678
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  83
  22Q GAIN WILD-TYPE  35 775
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   83
  22Q GAIN WILD-TYPE   35  775
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO               83                775
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED   128  18
  XP GAIN WILD-TYPE 788 110
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              146               898 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               110 
$`XP GAIN MUTATED`
TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A0CL TCGA-A2-A0CX TCGA-A2-A0D2 
      131.67        13.68        28.01        99.12        56.81        33.76 
TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 
       79.76        44.88        17.13         8.38        49.84        20.75 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A25E 
       21.90        18.61        31.73        20.25        42.44       105.34 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0DA TCGA-A7-A0DB 
       47.31        34.98        21.14        38.30        35.67        33.11 
TCGA-A7-A3J0 TCGA-A7-A5ZV TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P 
       10.29        12.10        17.03        53.98        32.05        10.98 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B 
        8.98        24.99         9.99        45.07        13.02        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A091 
       28.96        33.01        12.00        31.00       112.08        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09Q TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A3OD 
       17.95        41.98        25.02         5.72        38.53        14.83 
TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY 
       13.71         0.33         9.96         7.04         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B 
       66.77        81.63        62.04        71.80       106.78        98.27 
TCGA-AR-A0TR TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H 
        5.26        98.93        83.87        61.28        62.14       160.90 
TCGA-AR-A24Z TCGA-AR-A255 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0I5 
       79.00        58.92        20.38        54.74       143.38       149.59 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0BR 
      129.57       186.48       101.52        20.45        25.55        53.69 
TCGA-BH-A0BV TCGA-BH-A0DS TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18N 
       49.94         2.56        30.35        36.85        12.89        37.74 
TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1FC 
       55.63        91.99        82.85        12.00        25.81       114.15 
TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A130 
       26.14       130.16         9.63        11.93        11.77         3.16 
TCGA-C8-A275 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1JK 
        0.03        13.97        14.17        18.15        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XQ TCGA-D8-A1XW 
       20.09        13.32        18.58        21.83        16.41        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A10B 
       15.32        14.14        12.53        12.26        18.51        37.51 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A154 TCGA-E2-A15D 
       40.96        33.17        34.26        31.96        19.43        17.29 
TCGA-E2-A15K TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N6 
        9.04        53.62         8.28        34.92        12.85        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1RC TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL 
       13.12        35.24        40.24        29.72        12.33         0.79 
TCGA-EW-A1IY TCGA-EW-A1PB TCGA-GI-A2C9 TCGA-GM-A3XL TCGA-LL-A6FQ TCGA-LL-A73Y 
        8.48        19.99       109.87        69.30         2.63        15.68 
TCGA-OL-A5DA TCGA-OL-A5S0 TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       58.62        20.38         8.91         9.93        16.50        16.80 
TCGA-WT-AB44 TCGA-Z7-A8R6 
       29.03       107.05 

$`XP GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        98.99       107.93        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        27.12        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       44.28        17.52        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        18.21        50.47        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       19.20        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        32.75        49.48        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE 
       24.39        21.30        23.21        26.96        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13D 
       34.29        35.47        30.61        37.45        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW 
       13.74        14.50        21.17        17.92        14.73        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 
       18.97        14.01        12.00         9.99         7.99        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
       15.06        36.95         0.99        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99        33.01        43.00        40.01        30.97 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       49.05        45.07        29.98        33.07         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        27.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         2.37        10.85         1.48        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92         2.27        32.45        16.31        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        80.28        61.35        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       50.24        55.33       102.58        99.25       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       90.58        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        32.91        19.20       111.32        73.64        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       86.66        42.35        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      101.95       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       43.07        17.23        37.81        76.21        63.62        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28        87.22        97.84        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        89.00        78.48        73.18        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       52.11        38.17        39.39        40.54        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       10.59        77.62        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      129.70        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        85.35        74.99        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        24.53        59.84        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS 
       44.05        61.68        35.67        48.69        27.19        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       45.57        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT 
       13.91        48.23        17.26        15.65         3.22        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        13.61        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       30.28        37.55        66.05         7.36        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       69.93       113.82        42.28        55.69        49.58        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.66       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59        72.07        28.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       57.83        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
        8.94        18.64        23.51         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       21.76         9.44        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        12.66         0.39         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
        2.30         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        8.28         9.67         9.53         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 
       11.90        20.88        13.25        20.58        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        18.71        15.78 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JM 
       18.90        12.03        12.03        14.01        18.97        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.38        21.01        12.20        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69        15.55 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY 
       15.85        16.31         6.35        12.99        15.16        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         9.93        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U 
        0.76        10.09        13.08        33.37        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       38.24        38.60        33.30        43.33        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       18.51        25.41        27.12        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        23.34        22.82        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        17.42        19.40        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 
        5.52        15.72        30.61        26.56        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        36.82        12.00        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84         9.86        11.90        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09         1.12        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       22.75        41.03        12.89        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41        30.18        15.72        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70        13.81        14.40        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       14.79        22.26        16.08         7.46        14.50        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        14.73        14.07        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73        40.11        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        0.26        13.12        16.93        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       14.96        13.84        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        15.35        16.04       108.07 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.03              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           186.48            234.28 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            25.68             24.41 
[1] "0.0 - 186.5 (25.7)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED        12        7        2        1        56        32
  XP GAIN WILD-TYPE      77       74        6        2       297       213
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           0         21          4         10        5
  XP GAIN WILD-TYPE         2        129         25         53       15
                   vv
clus                STAGE TIS STAGE X
  XP GAIN MUTATED           0       0
  XP GAIN WILD-TYPE         1      13
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 7                74
  STAGE IB                 2                 6
  STAGE II                 1                 2
  STAGE IIA               56               297
  STAGE IIB               32               213
  STAGE III                0                 2
  STAGE IIIA              21               129
  STAGE IIIB               4                25
  STAGE IIIC              10                53
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    28  98  19   5
  XP GAIN WILD-TYPE 244 518 111  35
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              28               244
  T2              98               518
  T3              19               111
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP GAIN MUTATED    74  44  19  11
  XP GAIN WILD-TYPE 427 306  98  64
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              74               427
  N1              44               306
  N2              19                98
  N3              11                64
[1] 4 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   129   5
  XP GAIN WILD-TYPE 750  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    129    5
  XP GAIN WILD-TYPE  750   16
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0             129               750
  1               5                16
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED   149   1
  XP GAIN WILD-TYPE 902  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    149    1
  XP GAIN WILD-TYPE  902   10
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE             149               902
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP GAIN MUTATED                            1                           122
  XP GAIN WILD-TYPE                          0                           641
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP GAIN MUTATED                               11                   3
  XP GAIN WILD-TYPE                            181                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP GAIN MUTATED                       1                                3
  XP GAIN WILD-TYPE                     3                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XP GAIN MUTATED                    3              6
  XP GAIN WILD-TYPE                 14             42
D40V8, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                122               641
  INFILTRATING LOBULAR CARCINOMA                11               181
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 6                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    48 102
  XP GAIN WILD-TYPE 240 672
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     48  102
  XP GAIN WILD-TYPE  240  672
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               48               240
  YES             102               672
[1] 2 2
[1] FALSE
D40V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  1     6
  XP GAIN WILD-TYPE                                0    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          31    91
  XP GAIN WILD-TYPE                       139   645
D40V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     31               139
  WHITE                                         91               645
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3 117
  XP GAIN WILD-TYPE  35 741
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3  117
  XP GAIN WILD-TYPE   35  741
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                35
  NOT HISPANIC OR LATINO             117               741
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   119  13
  XQ GAIN WILD-TYPE 797 115
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              132               912 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13               115 
$`XQ GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0D2 
       13.68        28.01        73.84        24.79        56.81        33.76 
TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        44.88         8.38        49.84        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25E TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 
       31.73        20.25       105.34        47.31        34.98        21.14 
TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD 
       38.30        33.11        22.32        10.29        14.70        14.50 
TCGA-A7-A5ZV TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W 
       12.10        53.98        32.05        10.98         8.98         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08T 
       45.07        13.02        38.01        28.96        33.01       112.08 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09Q TCGA-A8-A09W 
       33.01        17.95        41.98        12.00        25.02         0.99 
TCGA-AC-A2BK TCGA-AC-A3OD TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0FT TCGA-AN-A0FX 
       38.53        14.83        13.71         0.33         7.04         0.33 
TCGA-AN-A0FY TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0JM 
        0.33        66.77        81.63        32.78        52.18        71.80 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TW TCGA-AR-A1AV 
      106.78        98.27        48.36        70.39        98.93        61.28 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A5QM TCGA-B6-A0I2 
      104.28        87.22        79.00        72.76        54.74       143.38 
TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-BH-A0AW TCGA-BH-A0AY 
      149.59       129.57       186.48       101.52        20.45        25.55 
TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0HQ 
       48.23         2.56         9.63        24.43        30.35        36.85 
TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1ET 
       50.79        23.05        37.74        55.63        91.99        82.85 
TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12M 
       25.81       114.15        26.14         9.63        11.93        11.77 
TCGA-C8-A1HG TCGA-C8-A274 TCGA-C8-A275 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JD 
       11.34         9.53         0.03        13.97        14.17        18.15 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27V 
       13.32        18.58        16.41        12.66        15.32        12.53 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14V 
       12.26        18.51        37.51        40.96        33.17        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A15D TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E2-A9RU 
       31.96        28.60        17.29        53.62         8.28        12.85 
TCGA-E9-A1N6 TCGA-E9-A1RC TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL TCGA-EW-A1IY 
       13.48        40.24        29.72        12.33         0.79         8.48 
TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GI-A2C9 TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-OL-A5S0 
       23.11        19.99       109.87         2.63        15.68        20.38 
TCGA-OL-A66I TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-Z7-A8R6 
       23.47         8.91         9.93        16.50        16.80       107.05 

$`XQ GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       99.12       114.81        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        98.99       107.93        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        27.12        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.28        17.52        17.13        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       20.75        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        42.44        17.19        18.15        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        32.75        49.48 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       21.73        20.61        11.34        10.59        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        17.03         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O 
       19.99        18.97        18.97        14.01        12.00         9.99 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A 
        7.99        24.99        18.05        15.06        36.95         0.99 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A099 
        0.99        33.01        43.00        40.01        30.97         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         1.02         8.98        19.04        15.02 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       32.45        16.31        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.62         2.96         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.36         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        80.28        61.35        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       58.95        29.13        21.40        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D 
      102.58        99.25       108.72       108.03        90.58        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
       73.64         5.26        74.79        86.66        42.35        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86       107.24        65.36       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       76.11        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        76.21        63.62        62.14        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        78.48        73.18        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        20.38        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.63        18.35        21.47       113.79       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        68.94        58.88        43.59        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        74.99        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       24.53        59.84        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT 
       22.13        13.91        17.26        15.65         3.22        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ 
       44.81        46.19        32.58        24.49        31.00        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       90.84        26.66        72.56        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU 
        7.36        51.39        51.16        69.93       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        49.58        17.69        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       18.64        23.51         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         9.50        12.20         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        18.71        15.78        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 
       19.40        20.38        21.01        12.20        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        15.55        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       28.87        47.15        44.68        38.24        38.60        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       43.33        32.02        18.51        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        60.53        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        26.56        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        32.09         1.12        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        22.75        41.03        12.89        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.69        27.22         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        14.70        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.43        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 
       14.47        14.79        22.26        16.08         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        22.32        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       28.21        19.73        40.11        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26        13.12        16.93        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           186.48            234.28 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           25.680            24.325 
[1] "0.0 - 186.5 (25.7)" "0.0 - 234.3 (24.3)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         8        7        2        1        54        28
  XQ GAIN WILD-TYPE      81       74        6        2       299       217
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           0         16          5          9        5
  XQ GAIN WILD-TYPE         2        134         24         54       15
                   vv
clus                STAGE TIS STAGE X
  XQ GAIN MUTATED           0       0
  XQ GAIN WILD-TYPE         1      13
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  8                81
  STAGE IA                 7                74
  STAGE IB                 2                 6
  STAGE II                 1                 2
  STAGE IIA               54               299
  STAGE IIB               28               217
  STAGE III                0                 2
  STAGE IIIA              16               134
  STAGE IIIB               5                24
  STAGE IIIC               9                54
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    27  89  14   5
  XQ GAIN WILD-TYPE 245 527 116  35
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              27               245
  T2              89               527
  T3              14               116
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    68  39  16  11
  XQ GAIN WILD-TYPE 433 311 101  64
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              68               433
  N1              39               311
  N2              16               101
  N3              11                64
[1] 4 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   115   5
  XQ GAIN WILD-TYPE 764  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    115    5
  XQ GAIN WILD-TYPE  764   16
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0             115               764
  1               5                16
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   134   1
  XQ GAIN WILD-TYPE 917  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    134    1
  XQ GAIN WILD-TYPE  917   10
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE             134               917
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ GAIN MUTATED                            1                           112
  XQ GAIN WILD-TYPE                          0                           651
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ GAIN MUTATED                                9                   2
  XQ GAIN WILD-TYPE                            183                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ GAIN MUTATED                       1                                1
  XQ GAIN WILD-TYPE                     3                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XQ GAIN MUTATED                    3              5
  XQ GAIN WILD-TYPE                 14             43
D41V8, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                112               651
  INFILTRATING LOBULAR CARCINOMA                 9               183
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 5                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    43  92
  XQ GAIN WILD-TYPE 245 682
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     43   92
  XQ GAIN WILD-TYPE  245  682
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               43               245
  YES              92               682
[1] 2 2
[1] FALSE
D41V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     6
  XQ GAIN WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          30    80
  XQ GAIN WILD-TYPE                       140   656
D41V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     30               140
  WHITE                                         80               656
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3 103
  XQ GAIN WILD-TYPE  35 755
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3  103
  XQ GAIN WILD-TYPE   35  755
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                35
  NOT HISPANIC OR LATINO             103               755
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   196  39
  1P LOSS WILD-TYPE 720  89
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              235               809 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               39                89 
$`1P LOSS MUTATED`
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CW 
      131.67         9.96        39.32       121.94        75.55       107.93 
TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SV 
       25.22       134.40        79.76        35.05        63.29        27.12 
TCGA-A2-A0T4 TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW 
       20.52        18.21        50.47        21.90        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A25C TCGA-A2-A3KC TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CJ 
       60.72        17.19        20.88        29.98        21.90        30.61 
TCGA-A7-A0DC TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06U 
       29.79        14.73        12.10        13.02        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G 
       26.01        17.03         9.01        43.00        18.97        18.97 
TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
        8.98        15.06        38.01        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       30.97         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 
       49.05        45.07         1.02        25.02        14.01        19.04 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM 
       21.04        27.02        17.03         2.37        38.53        26.04 
TCGA-AC-A3BB TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
       32.45        20.19         0.33         0.33         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN 
        2.96         6.51         0.33         6.44         7.00         7.17 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        0.30         0.33         0.33        80.28        66.77        95.70 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A12A TCGA-AO-A1KP 
       26.04        20.32        21.53        50.24        90.58        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AP 
       61.87         0.53         5.65        73.64        83.87        39.98 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A250 TCGA-AR-A254 
       63.62       160.90        87.22        76.01        89.00        72.76 
TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG 
       54.21        39.39        16.04        12.13       129.57       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RP 
      176.98       110.14       211.56        81.17       162.05       102.77 
TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KF 
      100.70        79.63        18.35        21.47       113.79       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A40B TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 
       73.51       139.17       103.63        40.83        48.36        56.94 
TCGA-BH-A0BA TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E2 TCGA-BH-A0E9 
       37.22        49.94        41.75        44.02        14.30        46.19 
TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HW 
       24.49        30.35        10.78        23.08        12.89        51.32 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18T 
       23.93         8.81        90.84        26.66        30.28         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FC 
       51.39        69.93        42.28        12.00        24.66       114.15 
TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5J0 
       74.73        45.63        83.31       130.16        10.52        23.51 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A138 TCGA-C8-A1HK TCGA-C8-A1HL 
       11.77        12.66         2.24         4.08        12.03        10.42 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-D8-A142 
        0.36         8.28         9.53        12.20         0.03        13.97 
TCGA-D8-A146 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       21.14        18.90        12.03        18.97        20.09        19.40 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       15.22        14.73        16.41        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27T 
       15.16        15.32         9.93        14.14        14.43        13.08 
TCGA-D8-A27W TCGA-D8-A73U TCGA-E2-A107 TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14V 
       12.26        16.18        34.42        28.44        44.68        34.26 
TCGA-E2-A15R TCGA-E2-A1IH TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-E2-A576 TCGA-E9-A1NA 
       17.06        33.73        18.87        16.93        34.29        36.56 
TCGA-E9-A1ND TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A1RG 
       12.59         9.86         2.56         3.02        40.24        21.27 
TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 
       39.09        12.89         0.69        27.22         7.13         0.72 
TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OY 
       29.72        23.84        14.70        14.40        28.77        29.85 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR 
       52.96        23.11         6.15        10.52        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GM-A3NW TCGA-HN-A2NL TCGA-JL-A3YX 
       25.91        22.09         7.40       110.50         2.60        11.57 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RZ 
       17.06        15.32        22.26        14.07         2.10        22.32 
TCGA-OL-A66K TCGA-OL-A66N TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-WT-AB41 TCGA-WT-AB44 
       41.92        26.04         0.16        16.50        52.96        29.03 
TCGA-Z7-A8R5 
      108.07 

$`1P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        18.02        78.41        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
       24.79       114.81        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        98.99        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       61.58       101.72        80.28       107.61        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       34.29        31.82        61.94        24.72        99.19        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        42.44        18.15       105.34        10.59 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        83.01        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       35.47        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        21.17        17.92        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07I 
       17.98        31.00         1.02        53.98        19.99        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        18.05        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
        0.99       112.08        43.00        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T 
       41.98        12.00        29.98        33.07         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD 
       15.02         0.99        12.00        13.02         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95        10.85         5.72         1.48        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A049 TCGA-AN-A04C 
        0.03         1.12         1.32         2.30         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         9.96         7.36         0.16         0.33         0.33 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        5.65         7.96         7.59         6.28         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
       12.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB 
       21.40        52.18        37.48        22.36        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       50.86        72.00        76.77        21.37        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       28.37        14.73        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
      130.09        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32         5.26        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86       107.24        65.36       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       76.11        43.73        43.56        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       76.21        61.28        62.14        33.73        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       96.89        78.51        84.20         2.76       104.28        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       53.36        85.35        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        58.92        93.83       143.21        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       66.15        52.11        38.17        40.54        20.38        54.74 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       112.37        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      110.93       140.88        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       140.48        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      188.68       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
       58.88        43.59       170.17        85.35        74.99        68.12 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        24.53        59.84        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       46.95        39.55        39.16        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        25.71        24.85        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       11.67        49.05        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27         4.41        15.68         9.63        44.81        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        24.43        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        27.25        50.79         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         2.01         7.23        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V 
       72.56        37.74        55.63        37.55        66.05        51.16 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99       113.82        82.85        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FD 
       25.81        31.53        89.16        97.48       120.62        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O 
       72.07        28.14        26.14        38.60        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
        6.44        20.12       109.28         8.94        18.64         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         0.39         3.16         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.11        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 
        2.30         3.25         0.30         0.23         0.43         9.67 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        0.03         9.50         0.99         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        11.90        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK 
       18.71        15.78        18.15        12.03        14.01        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15        12.39        17.16        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       17.69        15.55         6.35        12.66        16.54        15.52 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.24        17.42        16.04        13.45        13.05         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        10.09        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        18.51        21.67         8.02        12.10        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F 
       27.52        46.59        40.41        37.51        40.11        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        32.02        31.96        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        13.02        19.56        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 
        8.28        30.61        34.92        26.56        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       32.88        36.82        13.48        12.00        13.12        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        35.24        25.84        11.90        28.27        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        6.12         2.76        21.21        32.09        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       12.53        13.32        22.75        41.03        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       17.06         1.94        24.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       30.18        15.72        12.33         0.79        13.81        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       16.57        15.68        25.94        22.82        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       41.13        39.78        29.82        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS 
       18.90        19.99        13.94        14.43        34.55        52.73 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        62.43        11.84        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        14.79         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        7.46        14.50        14.70        12.36        14.73        27.91 
TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       23.47        65.62        42.77        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        13.12        16.93        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        15.35        14.96        13.84        13.94        17.03 
TCGA-UU-A93S TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        11.41        15.35        16.04       107.05 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.03              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           211.56            234.28 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            22.32             24.79 
[1] "0.0 - 211.6 (22.3)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED        13       13        1        1        77        43
  1P LOSS WILD-TYPE      76       68        7        2       276       202
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           1         42         17         19        7
  1P LOSS WILD-TYPE         1        108         12         44       13
                   vv
clus                STAGE TIS STAGE X
  1P LOSS MUTATED           0       5
  1P LOSS WILD-TYPE         1       8
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 13                76
  STAGE IA                13                68
  STAGE IB                 1                 7
  STAGE II                 1                 2
  STAGE IIA               77               276
  STAGE IIB               43               202
  STAGE III                1                 1
  STAGE IIIA              42               108
  STAGE IIIB              17                12
  STAGE IIIC              19                44
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    50 139  27  22
  1P LOSS WILD-TYPE 222 477 103  18
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              50               222
  T2             139               477
  T3              27               103
  T4              22                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    94  79  36  24
  1P LOSS WILD-TYPE 407 271  81  51
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              94               407
  N1              79               271
  N2              36                81
  N3              24                51
[1] 4 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   199   7
  1P LOSS WILD-TYPE 680  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    199    7
  1P LOSS WILD-TYPE  680   14
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0             199               680
  1               7                14
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   237   2
  1P LOSS WILD-TYPE 814   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    237    2
  1P LOSS WILD-TYPE  814    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE             237               814
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P LOSS MUTATED                            1                           176
  1P LOSS WILD-TYPE                          0                           587
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P LOSS MUTATED                               43                   2
  1P LOSS WILD-TYPE                            149                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P LOSS MUTATED                       0                                5
  1P LOSS WILD-TYPE                     4                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1P LOSS MUTATED                    2             10
  1P LOSS WILD-TYPE                 15             38
D42V8, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                176               587
  INFILTRATING LOBULAR CARCINOMA                43               149
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                25
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                10                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    65 174
  1P LOSS WILD-TYPE 223 600
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     65  174
  1P LOSS WILD-TYPE  223  600
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               65               223
  YES             174               600
[1] 2 2
[1] FALSE
D42V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    14
  1P LOSS WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          36   154
  1P LOSS WILD-TYPE                       134   582
D42V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                46
  BLACK OR AFRICAN AMERICAN                     36               134
  WHITE                                        154               582
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 183
  1P LOSS WILD-TYPE  32 675
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  183
  1P LOSS WILD-TYPE   32  675
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                32
  NOT HISPANIC OR LATINO             183               675
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    40  10
  1Q LOSS WILD-TYPE 876 118
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               50               994 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               118 
$`1Q LOSS MUTATED`
TCGA-A2-A0CW TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4S3 
      107.93        18.21        50.47        17.36        60.72        21.90 
TCGA-A7-A0DC TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A08J TCGA-A8-A08S TCGA-A8-A09N 
       29.79        29.03         9.01        37.05        33.01         1.02 
TCGA-AC-A3BB TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0XS TCGA-AN-A0XU 
       32.45         2.96         6.51         0.33         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0U2 
       66.77        95.70        82.62         0.53        73.64        83.87 
TCGA-AR-A24H TCGA-AR-A24T TCGA-B6-A0IG TCGA-B6-A0RL TCGA-BH-A0B6 TCGA-BH-A0BV 
      160.90        76.01       146.50        81.17        56.94        49.94 
TCGA-BH-A0E2 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0HW TCGA-BH-A1FC TCGA-BH-A1FE 
       14.30        30.35        10.78        51.32       114.15        74.73 
TCGA-BH-A204 TCGA-BH-A42T TCGA-C8-A138 TCGA-C8-A27A TCGA-D8-A1XQ TCGA-D8-A1XU 
       83.31        10.52         4.08        12.20        16.41        12.99 
TCGA-D8-A1XZ TCGA-E2-A15R TCGA-E9-A1ND TCGA-E9-A1RC TCGA-E9-A247 TCGA-EW-A1J6 
       15.32        17.06        12.59        40.24        27.22        28.77 
TCGA-HN-A2NL TCGA-OL-A5RZ 
        2.60        22.32 

$`1Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       98.99        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        17.03        53.98        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        12.00         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        5.72         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.36         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R 
        5.33         5.59        80.28        61.35        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KQ 
       57.30        48.36        41.62        28.37        14.73        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       111.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        74.79        86.66        42.35        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       76.21        61.28        63.62        62.14        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       87.22        97.84        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        89.00        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH 
       12.13       220.90       129.57        50.70        65.72       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       211.56        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        74.99        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       24.53        59.84        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        45.57        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        24.43        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        13.61        36.85        12.89        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
        7.36        51.39        51.16        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       57.83       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
        8.94        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.05         4.11        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.50         0.99         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69        15.55 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31         6.35        15.16        12.66        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       32.02        31.96        28.60        18.51        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       13.02        19.56        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         8.28        30.61        34.92        26.56 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        36.56        39.55        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02         2.76        21.21        32.09        32.09 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       41.03        12.89        23.51        20.71        17.06         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.79        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        14.70        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.73        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        16.50        13.12        16.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.33              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           160.90            234.28 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            28.90             24.46 
[1] "0.3 - 160.9 (28.9)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         3        5        0        0        15        12
  1Q LOSS WILD-TYPE      86       76        8        3       338       233
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0         10          2          3        1
  1Q LOSS WILD-TYPE         2        140         27         60       19
                   vv
clus                STAGE TIS STAGE X
  1Q LOSS MUTATED           0       0
  1Q LOSS WILD-TYPE         1      13
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 5                76
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               15               338
  STAGE IIB               12               233
  STAGE III                0                 2
  STAGE IIIA              10               140
  STAGE IIIB               2                27
  STAGE IIIC               3                60
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    14  28   5   4
  1Q LOSS WILD-TYPE 258 588 125  36
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              14               258
  T2              28               588
  T3               5               125
  T4               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    18  19   9   5
  1Q LOSS WILD-TYPE 483 331 108  70
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              18               483
  N1              19               331
  N2               9               108
  N3               5                70
[1] 4 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    47   1
  1Q LOSS WILD-TYPE 832  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     47    1
  1Q LOSS WILD-TYPE  832   20
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              47               832
  1               1                20
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                   0    1
  1Q LOSS MUTATED     51    0
  1Q LOSS WILD-TYPE 1000   11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     51    0
  1Q LOSS WILD-TYPE 1000   11
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              51              1000
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q LOSS MUTATED                            0                            43
  1Q LOSS WILD-TYPE                          1                           720
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q LOSS MUTATED                                5                   1
  1Q LOSS WILD-TYPE                            187                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q LOSS MUTATED                       0                                1
  1Q LOSS WILD-TYPE                     4                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1Q LOSS MUTATED                    0              1
  1Q LOSS WILD-TYPE                 17             47
D43V8, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 43               720
  INFILTRATING LOBULAR CARCINOMA                 5               187
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 1                47
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    16  35
  1Q LOSS WILD-TYPE 272 739
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     16   35
  1Q LOSS WILD-TYPE  272  739
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               16               272
  YES              35               739
[1] 2 2
[1] FALSE
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     3
  1Q LOSS WILD-TYPE                                1    57
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           9    32
  1Q LOSS WILD-TYPE                       161   704
D43V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                57
  BLACK OR AFRICAN AMERICAN                      9               161
  WHITE                                         32               704
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  37
  1Q LOSS WILD-TYPE  37 821
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   37
  1Q LOSS WILD-TYPE   37  821
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              37               821
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED   157  19
  2P LOSS WILD-TYPE 759 109
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              176               868 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               109 
$`2P LOSS MUTATED`
TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0EO 
      129.14        11.44        75.55        75.25        98.99        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX 
       35.05        34.29        27.12        21.67        17.36        60.72 
TCGA-A2-A25B TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A2KD 
       42.44        24.39        35.31        29.79        25.15        22.32 
TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B 
       11.28        10.42        13.02        26.01         1.02        43.00 
TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F 
       18.97        10.98         8.98         9.99        38.01        33.01 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C 
       37.05        31.00        33.01        30.97        12.00         1.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 
        1.02        25.02        19.04        19.04        21.04        27.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A62V 
       17.03         2.37        99.35        55.43        26.04        11.44 
TCGA-AC-A7VC TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        0.03         0.33         9.96         0.33         7.00         7.59 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT TCGA-AO-A03L 
        7.04         0.36         0.33         0.30         0.33        80.28 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI TCGA-AO-A12A TCGA-AO-A1KS 
       61.35        95.70        21.40        50.24        90.58         0.53 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AM 
       17.79         5.65        32.91       107.24       114.02        76.11 
TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V 
       43.73        37.81       160.90        50.89        87.22        85.35 
TCGA-AR-A24W TCGA-AR-A2LK TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A1KC 
       50.96        54.21       112.37       176.98        81.17        43.59 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA TCGA-BH-A0BT TCGA-BH-A0BV 
       73.51        68.12        40.83        37.22        45.57        49.94 
TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 
       42.90         4.41        14.30        24.49        31.00        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       41.00        52.96        12.89        51.32        27.25        50.79 
TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1FN TCGA-BH-A5J0 
        7.23        55.63       113.82        42.28        72.07        23.51 
TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A3M7 
        5.26        12.66        12.66         4.08        11.34         0.03 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JD TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1X6 
       13.97        21.14        18.15        18.97        21.01        17.79 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY 
       27.58        18.15        21.83        15.85        15.16        16.54 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14Z 
        9.93        14.14        13.08        44.68        38.60        18.51 
TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ 
       27.12        20.71        18.21        12.92        14.07        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 TCGA-E9-A1N6 
       17.10        33.73        22.19        16.93        32.88        13.48 
TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RG 
       35.24         2.76        32.09        32.09        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A249 TCGA-E9-A3HO 
       35.64        12.53        41.03        23.51         7.13        26.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW 
       15.72        23.84        14.40        18.90        28.77        22.82 
TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW 
       29.85        23.11         7.86        10.52        25.91        22.09 
TCGA-EW-A423 TCGA-GI-A2C8 TCGA-LL-A6FR TCGA-LL-A73Y TCGA-PE-A5DD TCGA-PL-A8LX 
       10.16         7.40        16.08        15.68        64.21         0.16 
TCGA-S3-A6ZH TCGA-XX-A89A 
       16.93        16.04 

$`2P LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        42.81        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
      107.93         5.19       107.93        56.81        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        61.58        25.22       101.72       134.40       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       79.76        74.40        72.00        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.77        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.30        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        53.06        29.03        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
       32.05         9.99         7.99        24.99        45.07        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       12.00         9.99        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        33.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        9.99        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        15.02         0.99        14.01        12.00        13.02 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       38.53        40.57        36.99        38.79        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX 
        5.65         7.96         7.17         6.28         0.33         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        32.78        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       50.86        72.00        76.77        21.37        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      111.32        73.64         5.26        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86        65.36       101.95        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        43.07        17.23        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14        33.73        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       84.20         2.76       104.28        97.84        76.01        53.36 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        89.00        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       58.92        93.83       143.21        20.25        62.86        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      211.56        68.45       189.01       234.28        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       58.88       101.52       139.17       170.17        85.35        74.99 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       56.98        51.68        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.69        53.95        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       38.47        67.86        47.41        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        46.19        32.58        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI 
       15.16        37.78        35.51        24.56        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A0W3 
        5.85         2.50        13.61        36.85         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99        82.85        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
       20.12        10.52       109.28         8.94        18.64         9.63 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
        0.39         3.16         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       12.20         0.99         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       19.46        11.90        20.88        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       15.78        18.90        12.03        12.03        14.01        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        19.40        20.38        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       14.70        18.58        16.73        25.74        23.90        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW 
       15.55        16.41        16.31         6.35        12.99        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.32        15.52        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        10.09        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T 
       28.87        47.15        40.96        38.24        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       43.33        34.26        32.02        31.96        28.60        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        13.02        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        38.30        37.41        32.78        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       22.65         3.88        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.82        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.59        35.77        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC 
       34.95         2.56         6.12         3.02        21.21        40.24 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
        1.12         6.58        34.59        34.13        32.05        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        22.75        12.89        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       27.22         1.94        24.56         0.72        29.72         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41        30.18        12.33        14.70         0.79        13.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       15.39        12.20        39.72         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        15.68        25.94        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        29.82        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        13.94        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 
       55.00        52.73        34.03        17.49        23.51       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       14.70        14.47        14.79        22.26         2.63         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
        8.91        47.01        86.96         0.26         9.93        16.50 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       13.12        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35       108.07       107.05 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.03              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           176.98            234.28 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           23.095            24.755 
[1] "0.0 - 177.0 (23.1)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED        12       12        0        0        55        38
  2P LOSS WILD-TYPE      77       69        8        3       298       207
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1         32          6         13        7
  2P LOSS WILD-TYPE         1        118         23         50       13
                   vv
clus                STAGE TIS STAGE X
  2P LOSS MUTATED           0       3
  2P LOSS WILD-TYPE         1      10
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 12                77
  STAGE IA                12                69
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               55               298
  STAGE IIB               38               207
  STAGE III                1                 1
  STAGE IIIA              32               118
  STAGE IIIB               6                23
  STAGE IIIC              13                50
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    38 108  23   9
  2P LOSS WILD-TYPE 234 508 107  31
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              38               234
  T2             108               508
  T3              23               107
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    81  51  29  16
  2P LOSS WILD-TYPE 420 299  88  59
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              81               420
  N1              51               299
  N2              29                88
  N3              16                59
[1] 4 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   143   8
  2P LOSS WILD-TYPE 736  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    143    8
  2P LOSS WILD-TYPE  736   13
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0             143               736
  1               8                13
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   177   2
  2P LOSS WILD-TYPE 874   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    177    2
  2P LOSS WILD-TYPE  874    9
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE             177               874
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P LOSS MUTATED                            0                           139
  2P LOSS WILD-TYPE                          1                           624
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P LOSS MUTATED                               24                   0
  2P LOSS WILD-TYPE                            168                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P LOSS MUTATED                       2                                6
  2P LOSS WILD-TYPE                     2                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2P LOSS MUTATED                    2              6
  2P LOSS WILD-TYPE                 15             42
D44V8, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                139               624
  INFILTRATING LOBULAR CARCINOMA                24               168
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 6                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    63 116
  2P LOSS WILD-TYPE 225 658
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     63  116
  2P LOSS WILD-TYPE  225  658
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               63               225
  YES             116               658
[1] 2 2
[1] FALSE
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0    12
  2P LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                          19   123
  2P LOSS WILD-TYPE                       151   613
D44V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12                48
  BLACK OR AFRICAN AMERICAN                     19               151
  WHITE                                        123               613
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10 128
  2P LOSS WILD-TYPE  28 730
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10  128
  2P LOSS WILD-TYPE   28  730
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                28
  NOT HISPANIC OR LATINO             128               730
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED   181  25
  2Q LOSS WILD-TYPE 735 103
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              206               838 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               25               103 
$`2Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV 
      129.14        42.81        11.44        75.55        75.25        98.99 
TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW 
       80.28        35.05        34.29        27.12        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13E 
       60.72        33.93        24.39        35.31        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06T 
       25.15        11.28        10.42        13.02         1.02        53.06 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R 
       26.01         1.02        43.00        18.97        10.98         8.98 
TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
        9.99        38.01        33.01        12.00        37.05        31.00 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09Q 
       33.01        30.97        12.00         1.02         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E 
       19.04        19.04        21.04        27.02        17.03         2.37 
TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC 
       99.35        55.43        26.04        11.44        13.58         0.03 
TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT 
        0.33         9.96         0.33         7.00         7.59         7.04 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT TCGA-AO-A03L 
        0.36         0.33         0.33         0.30         0.33        80.28 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JI TCGA-AO-A12A 
       61.35        95.70        21.40        72.00        50.24        90.58 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TS 
        0.53        17.79         5.65         2.56        32.91        74.79 
TCGA-AR-A0TV TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A1AY 
       42.35       114.02        76.11        43.73        37.81        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK 
      160.90        50.89        87.22        85.35        50.96        54.21 
TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A1KC 
       12.13       112.37       176.98        81.17       131.21        43.59 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA TCGA-BH-A0BT 
       73.51       139.17        68.12        40.83        37.22        45.57 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0EB 
       49.94        42.90         4.41        14.30         9.63        24.49 
TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW 
       31.00        23.08        41.00        52.96        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV 
       27.25         7.23        55.63       113.82        42.28        12.00 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A5IZ 
       97.48       114.15        45.63        72.07        26.14        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 TCGA-C8-A1HF 
       23.51         5.26        12.66        12.66         4.08        10.92 
TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A142 
       11.34        12.03         8.28         0.03        20.88        13.97 
TCGA-D8-A146 TCGA-D8-A1JI TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ 
       21.14        18.97        17.79        27.58        18.15        21.83 
TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27T 
       15.85        15.16        16.54         9.93        14.14        13.08 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A15E 
       44.68        38.60        31.96        18.51        27.12        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH 
       18.21        12.92        14.07        60.53        17.10        33.73 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NF 
       33.70        22.19        16.93        32.88        13.48        35.24 
TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RG 
        9.86         2.76        32.09        32.09        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A249 TCGA-E9-A3HO 
       35.64        12.53        41.03        23.51         7.13        26.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW 
       15.72        23.84        14.40        18.90        28.77        22.82 
TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW 
       29.85        23.11         7.86        10.52        25.91        22.09 
TCGA-EW-A423 TCGA-GM-A2DF TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-LL-A6FR TCGA-LL-A7SZ 
       10.16        70.85        72.03         2.60        16.08        14.70 
TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A6VO TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH 
       12.36        22.32        28.21        64.21         0.16        16.93 
TCGA-S3-AA14 TCGA-XX-A89A 
       14.96        16.04 

$`2Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        40.14        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       13.68        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58        25.22       101.72       134.40       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       74.40        72.00        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       21.30        23.21        26.96        21.14        21.90        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       31.73        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.29        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R 
       11.05        10.29         9.37         8.75        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       29.03        31.00        17.03        53.98         9.01        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S 
       18.97        14.01        12.00        32.05         9.99         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99        45.07        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R 
        0.99        28.96        19.96         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
       12.00         9.99         9.99        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       29.98        33.07         8.98        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
       12.00        13.02         0.99        38.04         0.95        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK 
        5.72         1.48        38.53        40.57        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       24.79         1.55        13.71        17.42        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        6.44         5.65         7.96         7.17         6.28         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        32.78        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        76.77        21.37        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78       108.03 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        70.39        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09        15.62        32.52        19.20       111.32        73.64 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        86.66        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       52.77        51.25        48.82        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L 
       17.23        76.21        61.28        63.62        62.14        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       96.89        78.51        84.20         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       76.01        53.36        83.77        79.00        89.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       211.56        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
       58.88       101.52       170.17        85.35        74.99       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        24.53        59.84        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       46.95        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       51.68        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0E9 
       67.86        47.41        16.27        15.68        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       35.51        24.56        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       13.61        36.85        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       42.35        44.81        23.05         8.81         2.01        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       90.84        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       82.85        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       36.92        63.35        55.00       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A8FY 
       20.12        10.52       109.28         8.94         9.63         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12Z 
       12.66        11.77        12.66        12.66        12.66         0.39 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16         2.24         1.87         1.12         1.05         4.11 
TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       12.33        11.28         0.16        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.23         0.36         0.43         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.50        12.20         0.99         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        11.90        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        23.90        12.39        17.16        15.22        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS 
       14.50        19.92        17.69        15.55        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 
        6.35        12.99        12.66        15.32        15.52        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.10        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       28.60        25.41        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       14.79        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        38.30        37.41        32.78 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       18.87       106.75       102.61         8.75        43.04         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       15.72         8.28        30.61        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       12.85        34.82        36.82        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        12.59        35.77        25.84        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC 
       34.95         2.56         6.12         3.02        21.21        40.24 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
        1.12         6.58        34.59        34.13        32.05        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        22.75        12.89        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       27.22         1.94        24.56         0.72        29.72         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41        30.18        12.33        14.70         0.79        13.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       15.39        12.20        39.72         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        15.68        25.94        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        29.82        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        13.94        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 
       55.00        52.73        34.03        17.49        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.79        22.26         2.63        15.68         7.46        14.50 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.73        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       41.92        42.77        26.04        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
       40.11         8.91        47.01        86.96         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       16.50        13.12        16.80        15.39        13.84        15.35 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35       108.07       107.05 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           176.98            234.28 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           23.095            24.755 
[1] "0.0 - 177.0 (23.1)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED        14       14        0        1        65        43
  2Q LOSS WILD-TYPE      75       67        8        2       288       202
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1         37          7         14        8
  2Q LOSS WILD-TYPE         1        113         22         49       12
                   vv
clus                STAGE TIS STAGE X
  2Q LOSS MUTATED           0       3
  2Q LOSS WILD-TYPE         1      10
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                14                67
  STAGE IB                 0                 8
  STAGE II                 1                 2
  STAGE IIA               65               288
  STAGE IIB               43               202
  STAGE III                1                 1
  STAGE IIIA              37               113
  STAGE IIIB               7                22
  STAGE IIIC              14                49
  STAGE IV                 8                12
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    45 123  29  11
  2Q LOSS WILD-TYPE 227 493 101  29
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              45               227
  T2             123               493
  T3              29               101
  T4              11                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    94  62  33  17
  2Q LOSS WILD-TYPE 407 288  84  58
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              94               407
  N1              62               288
  N2              33                84
  N3              17                58
[1] 4 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   168   8
  2Q LOSS WILD-TYPE 711  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    168    8
  2Q LOSS WILD-TYPE  711   13
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0             168               711
  1               8                13
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   207   2
  2Q LOSS WILD-TYPE 844   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    207    2
  2Q LOSS WILD-TYPE  844    9
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE             207               844
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q LOSS MUTATED                            0                           163
  2Q LOSS WILD-TYPE                          1                           600
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q LOSS MUTATED                               25                   2
  2Q LOSS WILD-TYPE                            167                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q LOSS MUTATED                       2                                7
  2Q LOSS WILD-TYPE                     2                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2Q LOSS MUTATED                    2              8
  2Q LOSS WILD-TYPE                 15             40
D45V8, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                163               600
  INFILTRATING LOBULAR CARCINOMA                25               167
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    67 142
  2Q LOSS WILD-TYPE 221 632
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     67  142
  2Q LOSS WILD-TYPE  221  632
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               67               221
  YES             142               632
[1] 2 2
[1] FALSE
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0    15
  2Q LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                          30   135
  2Q LOSS WILD-TYPE                       140   601
D45V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                45
  BLACK OR AFRICAN AMERICAN                     30               140
  WHITE                                        135               601
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11 151
  2Q LOSS WILD-TYPE  27 707
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11  151
  2Q LOSS WILD-TYPE   27  707
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                27
  NOT HISPANIC OR LATINO             151               707
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   155  26
  3P LOSS WILD-TYPE 761 102
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              181               863 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26               102 
$`3P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T 
      129.14       131.67        42.81        31.79        19.20        73.84 
TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       87.25        99.12        75.25       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0T3 TCGA-A2-A0YE 
       34.55        25.22        80.28        79.76        49.84        18.21 
TCGA-A2-A0YT TCGA-A2-A1G1 TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0CJ 
       23.77        19.20        47.31        26.96        35.31        30.61 
TCGA-A7-A13D TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A6VW TCGA-A7-A6VX 
       31.73        24.26        22.32        17.92         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A08O 
        8.75        29.03         1.02        18.97        12.00        31.00 
TCGA-A8-A09M TCGA-AC-A2BK TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A041 
       33.07        38.53        50.70        14.83         1.12         0.23 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT 
        1.78         1.71         0.33         7.96         7.59         7.04 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 
        0.33        80.28        61.35        95.70        47.87        21.40 
TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A124 TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AR-A0TP 
       21.53        26.24       102.58         0.53       130.09       111.32 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ 
       86.66        64.83       101.95        83.87        75.55        43.07 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO 
       97.84        76.01        78.48        58.92        93.83        39.39 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0WS TCGA-B6-A0WW 
      129.57       146.50       112.37       176.98        97.48        18.35 
TCGA-B6-A0WY TCGA-B6-A1KI TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW 
      113.79        73.51        51.68        24.85        21.70        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0HA 
       49.05        44.02        22.13        48.23         4.41        52.96 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18T 
       12.89        51.32         5.59         8.81        26.66         7.36 
TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A42T 
       69.93        24.66        45.63        72.07        57.83        10.52 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HG 
       18.64        11.93         1.05         4.11        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A8HP TCGA-C8-A8HQ 
        0.16        12.03         2.30         0.23        13.02        12.49 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       14.17        17.49        18.15        12.03        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       19.40        18.58        18.15        21.83        14.50        19.92 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M 
        6.35        12.99        16.54        15.32         9.93        13.48 
TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 
        4.80        40.11        38.60        34.26        25.41        27.12 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LE 
       25.05        23.34        33.70        20.98        27.42        28.90 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NF 
       26.56        34.29        12.85        12.00        39.55        35.24 
TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A295 
        6.12        34.13        13.32        23.51         0.69         0.72 
TCGA-E9-A2JS TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A2FS 
       29.72        22.82        29.82        23.11         6.15        52.73 
TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-HN-A2NL 
       10.16         7.40       109.87        79.10        72.10         2.60 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RY 
       11.57         7.10        17.06        12.36        14.73        24.72 
TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-XX-A89A 
       20.38        41.92        26.04        13.12        16.93        16.04 
TCGA-Z7-A8R5 
      108.07 

$`3P LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68         7.96        39.32        28.01        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       18.02        78.41       121.94        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        75.55         5.19        98.99        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      101.72       134.40       107.61        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13         8.38        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       18.61        19.33        48.46        31.73        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       49.48        34.98        50.37        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
       21.30        23.21        21.14        21.90        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       35.47        37.45        35.67        33.11        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H 
       25.15        23.61        29.56        31.36        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        14.73        12.10        10.72        11.05        10.29 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        99.35        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR 
       12.26         1.68         8.22         0.03        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.33         0.33         0.62         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        6.44         5.65         7.00         7.17         6.28         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV 
       12.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V 
        5.59        66.77        81.63        68.75        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39        17.79        24.79        26.93         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56        32.91        19.20        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       74.79        42.35        98.93        55.86       107.24        65.36 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      114.02        85.97        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       76.11        43.73        43.56        39.98        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
      104.28        87.22        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        89.00        73.18        72.76       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       62.86        54.21        66.15        52.11        38.17        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ 
      131.21       157.41       188.68        79.63        21.47       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      101.52       139.17       170.17        85.35        74.99        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        37.22        32.02        18.21        25.71 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.95        45.57        49.94        41.75        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO 
       45.83        31.17        23.44        38.01        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       23.05         2.01         7.23        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.16        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        72.07       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       20.12       109.28         8.94        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
        4.08        12.33        11.28        10.42         3.25         0.30 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR 
        9.50        12.20         0.99         0.03         0.23        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       15.22        14.73        17.69        15.55        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.31        15.16        12.66        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       16.41         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        33.30        43.33        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       18.51        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
        3.88        22.19        11.08        54.18        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        40.47        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         8.28        30.61 
TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       34.92        34.82        32.88        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       36.56        12.59        35.77        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       28.27        34.95         2.56         3.02         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        32.09        40.24         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A 
       21.27        34.59        35.64        32.05        12.53        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       22.75        41.03        12.89        20.71        17.06        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        1.94         7.13        24.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        15.72        12.33        23.84        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       13.81        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GM-A2D9 
       25.91        22.09        34.03        17.49        23.51        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        83.34        75.02        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.43        11.84        21.24        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN 
       24.95        11.44        10.95        25.05        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        14.70        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        36.36        28.87        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       65.62        42.77        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        16.50        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       11.41        52.96        29.03        15.35       107.05 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.16              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           176.98            234.28 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.26             24.56 
[1] "0.2 - 177.0 (24.3)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED        11       12        1        0        62        55
  3P LOSS WILD-TYPE      78       69        7        3       291       190
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         22          3         11        3
  3P LOSS WILD-TYPE         2        128         26         52       17
                   vv
clus                STAGE TIS STAGE X
  3P LOSS MUTATED           0       3
  3P LOSS WILD-TYPE         1      10
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 11                78
  STAGE IA                12                69
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               62               291
  STAGE IIB               55               190
  STAGE III                0                 2
  STAGE IIIA              22               128
  STAGE IIIB               3                26
  STAGE IIIC              11                52
  STAGE IV                 3                17
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    29 130  20   3
  3P LOSS WILD-TYPE 243 486 110  37
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              29               243
  T2             130               486
  T3              20               110
  T4               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    87  62  18  13
  3P LOSS WILD-TYPE 414 288  99  62
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              87               414
  N1              62               288
  N2              18                99
  N3              13                62
[1] 4 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   146   3
  3P LOSS WILD-TYPE 733  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    146    3
  3P LOSS WILD-TYPE  733   18
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             146               733
  1               3                18
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   183   0
  3P LOSS WILD-TYPE 868  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    183    0
  3P LOSS WILD-TYPE  868   11
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             183               868
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P LOSS MUTATED                            0                           149
  3P LOSS WILD-TYPE                          1                           614
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P LOSS MUTATED                               19                   1
  3P LOSS WILD-TYPE                            173                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P LOSS MUTATED                       1                                3
  3P LOSS WILD-TYPE                     3                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3P LOSS MUTATED                    1              9
  3P LOSS WILD-TYPE                 16             39
D46V8, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                149               614
  INFILTRATING LOBULAR CARCINOMA                19               173
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 9                39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    62 121
  3P LOSS WILD-TYPE 226 653
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     62  121
  3P LOSS WILD-TYPE  226  653
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               62               226
  YES             121               653
[1] 2 2
[1] FALSE
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0    16
  3P LOSS WILD-TYPE                                1    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          38   119
  3P LOSS WILD-TYPE                       132   617
D46V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     38               132
  WHITE                                        119               617
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2 160
  3P LOSS WILD-TYPE  36 698
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  160
  3P LOSS WILD-TYPE   36  698
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                36
  NOT HISPANIC OR LATINO             160               698
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    84  15
  3Q LOSS WILD-TYPE 832 113
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               99               945 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15               113 
$`3Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CT 
      129.14        42.81        31.79        19.20        73.84        75.25 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ 
      107.93        56.81        34.55        25.22        80.28        79.76 
TCGA-A2-A0YE TCGA-A2-A0YT TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A26F TCGA-A7-A2KD 
       18.21        23.77        47.31        26.96        24.26        22.32 
TCGA-A7-A4SF TCGA-A7-A6VY TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A08O 
       17.92         8.75        29.03         1.02        18.97        31.00 
TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0FJ 
       50.70        14.83         1.12         1.78         0.33         7.96 
TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03P TCGA-AO-A0JA TCGA-AO-A124 TCGA-AO-A1KS 
        7.04         0.33        95.70        21.53       102.58         0.53 
TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A251 TCGA-B6-A0IG 
       86.66        83.87        75.55        43.07        78.48       146.50 
TCGA-B6-A1KI TCGA-BH-A0B9 TCGA-BH-A0BJ TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0HW 
       73.51        51.68        21.70        49.05        44.02        51.32 
TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1FM TCGA-BH-A1FU 
        8.81        26.66         7.36        69.93        45.63        72.07 
TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK 
       57.83        11.93         1.05        10.92        11.34        12.03 
TCGA-C8-A1HM TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ 
        2.30        14.17        17.49        18.15        12.03        20.09 
TCGA-D8-A1JM TCGA-D8-A1XB TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       19.40        18.15         6.35        16.54        15.32         9.93 
TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A150 TCGA-E2-A15A 
        4.80        40.11        38.60        33.30        25.41        23.34 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1R4 
       20.98        27.42        26.56        34.29        12.85         6.12 
TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-EW-A1P5 
       34.13        23.51         0.69        27.22         0.72        23.11 
TCGA-GI-A2C9 TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A7T0 TCGA-OL-A66K TCGA-OL-A66N 
      109.87        11.57         7.10        12.36        41.92        26.04 
TCGA-S3-A6ZG TCGA-XX-A89A TCGA-Z7-A8R5 
       13.12        16.04       108.07 

$`3Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        75.55         5.19 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       98.99        67.33        33.76        61.58       101.72       134.40 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      107.61        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        48.46        31.73        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       49.48        34.98        50.37        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       29.79        31.73        20.19        25.15        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       31.36        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       10.72        11.05        10.29         9.37        10.42        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        5.72         1.48        38.53        99.35        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        26.04        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       32.45        16.31        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       20.19         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.59         7.17         6.28         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT 
       28.37        14.73        82.62        61.87        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       74.79        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36       101.95       114.02        85.97        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       33.73       160.90        50.89        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.72       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52       139.17       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       68.12       103.63        71.15        24.53        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       48.36        56.94        56.98        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05        51.39        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07       144.59        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.11         4.08        12.33        11.28         0.16        10.42 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        21.14        19.20        16.50        18.71        15.78 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        12.03        14.01        18.97        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       17.69        15.55        16.41        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        12.66        15.52        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 
        5.52        15.72         8.28        30.61        34.92        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       32.88        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       39.55        12.59        35.77        35.24        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        28.27        34.95         2.56         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        32.09        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
        6.58        21.27        34.59        35.64        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       13.32        39.09        22.75        41.03        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
       17.06         1.94         7.13        24.56        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.79        13.81        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.43 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        14.70        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O 
       20.38        26.70        23.47        65.62        42.77        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       29.03        15.35       107.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.33              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           146.50            234.28 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            23.51             24.59 
[1] "0.3 - 146.5 (23.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        9        0        0        36        30
  3Q LOSS WILD-TYPE      87       72        8        3       317       215
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         14          1          5        2
  3Q LOSS WILD-TYPE         2        136         28         58       18
                   vv
clus                STAGE TIS STAGE X
  3Q LOSS MUTATED           0       1
  3Q LOSS WILD-TYPE         1      12
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                87
  STAGE IA                 9                72
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               36               317
  STAGE IIB               30               215
  STAGE III                0                 2
  STAGE IIIA              14               136
  STAGE IIIB               1                28
  STAGE IIIC               5                58
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    13  76   9   1
  3Q LOSS WILD-TYPE 259 540 121  39
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              13               259
  T2              76               540
  T3               9               121
  T4               1                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    48  32  12   6
  3Q LOSS WILD-TYPE 453 318 105  69
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              48               453
  N1              32               318
  N2              12               105
  N3               6                69
[1] 4 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    83   2
  3Q LOSS WILD-TYPE 796  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     83    2
  3Q LOSS WILD-TYPE  796   19
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              83               796
  1               2                19
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   100   0
  3Q LOSS WILD-TYPE 951  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    100    0
  3Q LOSS WILD-TYPE  951   11
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE             100               951
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q LOSS MUTATED                            0                            83
  3Q LOSS WILD-TYPE                          1                           680
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q LOSS MUTATED                               12                   0
  3Q LOSS WILD-TYPE                            180                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q LOSS MUTATED                       0                                1
  3Q LOSS WILD-TYPE                     4                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3Q LOSS MUTATED                    0              4
  3Q LOSS WILD-TYPE                 17             44
D47V8, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 83               680
  INFILTRATING LOBULAR CARCINOMA                12               180
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 4                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    36  64
  3Q LOSS WILD-TYPE 252 710
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     36   64
  3Q LOSS WILD-TYPE  252  710
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               36               252
  YES              64               710
[1] 2 2
[1] FALSE
D47V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     9
  3Q LOSS WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          18    67
  3Q LOSS WILD-TYPE                       152   669
D47V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                51
  BLACK OR AFRICAN AMERICAN                     18               152
  WHITE                                         67               669
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  90
  3Q LOSS WILD-TYPE  38 768
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   90
  3Q LOSS WILD-TYPE   38  768
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              90               768
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   294  47
  4P LOSS WILD-TYPE 622  81
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              341               703 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               47                81 
$`4P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67        42.81        20.88        31.79        39.32 
TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV 
       28.01        18.02        99.12        24.79        75.55        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0SV TCGA-A2-A0T1 TCGA-A2-A0T3 
      107.93        67.33        79.76        27.12        17.13        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 
       20.75        18.21        21.67        18.61        17.36        19.20 
TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX 
       17.19        33.93        83.01        50.37         7.30        24.39 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.31        30.61        35.67        31.73        20.19        25.15 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZV 
       23.74        21.73        22.32        14.50        14.73        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06T 
       10.29         9.37        10.42         8.75         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A07B TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 
       31.00        26.01        43.00         9.99         8.98        15.06 
TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R 
       36.95        38.01        33.01        12.00         9.99         0.99 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09X 
       43.00        30.97         1.02        49.05        45.07        14.01 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A5XS 
        0.95         2.37        38.53         0.92        32.45         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
       11.44        13.71        17.42        13.58         0.03         1.12 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN 
        7.00         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         0.33         5.59 
TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JE 
       66.77        32.78        21.40        52.18        20.32        76.77 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
       71.80       102.58       108.03        90.58        64.04        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87         0.53        17.79        26.93       130.09         5.65 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
      111.32         5.26        55.86        65.36       101.95       114.02 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR 
       75.55        61.84        76.11        43.73        43.07        17.23 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24V 
       33.73       160.90        50.89        84.20       104.28        85.35 
TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A5QN 
       50.96        78.48        58.92        93.83        39.39        16.04 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH 
       10.59        77.62       220.90       129.57       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      176.98        18.77        84.59       110.14       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX 
      189.01        81.17       100.70       131.21        79.63        21.47 
TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      113.79        43.59        73.51        85.35        74.99        68.12 
TCGA-B6-A40B TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA 
      103.63        20.45        46.95        39.55        48.36        37.22 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       25.71        24.85        21.70        44.05        48.69        53.69 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DX 
       45.57        49.94        41.75        44.02        42.90        47.41 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0HI 
        4.41         9.63        46.19        24.49        23.08        20.38 
TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F 
       12.89        50.79         5.59        23.93        23.05         8.81 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV 
       55.63         7.36        51.39        51.16        42.28        12.00 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 
       25.81        97.48        24.66        33.17        72.07        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12P 
       57.83       130.16        18.64        23.51        11.93        11.77 
TCGA-C8-A12Z TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
        0.39         1.05         4.08         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP 
        2.30         0.43         0.03         9.50         0.99        13.02 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JE 
       11.90        20.88        13.97        19.20        16.50        18.90 
TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF 
       12.03        20.09        20.12        19.40        27.58        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU 
       14.73        21.83        14.50        15.55        15.85        12.99 
TCGA-D8-A1XW TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-D8-A73U 
       12.66        14.14        16.04        13.05        13.08        16.18 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14Z 
       47.15        44.68        40.96        38.24        38.60        18.51 
TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A1AZ 
       25.41        19.43        14.79        25.05        12.92        60.53 
TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 
       53.62        17.10        33.73        33.70        27.42        39.62 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
       18.87       106.75       102.61        34.92        26.56        12.85 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI 
       13.48        12.00        39.55        12.59        35.24         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A22E TCGA-E9-A22G 
        2.56        21.21        32.09        32.09        12.89        23.51 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.69         1.94         7.13        26.07        15.72        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW 
       14.70         0.79        39.72        18.90        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PD 
       29.85        40.41        23.11         7.86         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB 
       10.52        55.00        17.49         7.40       109.87        79.10 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A3XL TCGA-HN-A2NL 
       70.85        72.10        85.15       115.69        69.30         2.60 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR 
       11.84        11.57        11.44        15.32        14.79        16.08 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
        7.46        14.73        58.52        36.36        20.38        23.47 
TCGA-OL-A66K TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZH 
       41.92        28.21        86.96         0.16         9.93        16.93 
TCGA-S3-AA10 TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-WT-AB44 
       15.39        14.96        13.94        17.03        29.03 

$`4P LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
       14.37        43.43        48.10        14.27        47.24        13.68 
TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
        7.96        19.20        18.21       104.81        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
      136.73       114.81        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40        80.28       107.61        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        44.88        50.43        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        21.90        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        23.47        60.72        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        42.44        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        39.65        29.98        32.75        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       47.31        34.98        38.37        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        38.30        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       33.11        29.79        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       17.92        10.72        11.05        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       29.03         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       18.97        18.97        14.01        12.00        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 
        7.99        24.99         9.99        45.07        18.05        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
        0.99        28.96        19.96        37.05        31.00        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       33.01       112.08        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09K 
       12.00         9.99         9.99        12.00        50.04        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       27.02        17.03        38.04        10.85         5.72         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70        33.04         2.27        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV 
       14.99        16.57        19.79        23.24        24.79        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0FF 
        0.33         0.33         1.78         7.36         6.51         5.65 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.59         7.17         6.28         0.33         0.33         0.33 
TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33        80.28        61.35        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J6 
       68.75        47.87        58.95        29.13        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 
       21.37        26.24        50.24        62.04        55.33        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      108.72       106.78        98.27        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       14.73        82.62        70.39        24.79        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
        2.56        32.91        19.20        73.64        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 
       42.35        98.93        64.83       107.24        83.87        85.97 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
       52.77        51.25        48.82        43.56        39.98        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M 
       76.21        61.28        63.62        62.14        94.22        96.89 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       78.51         2.76        87.22        97.84        76.01        53.36 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE 
       83.77        79.00        89.00        73.18        72.76       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       40.54        20.38        54.74        20.45       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       12.13        50.70        65.72       126.12       110.93        68.45 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ 
       89.46       157.41        97.48       188.68        18.35       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
      139.17       170.17        71.15        24.53        59.84        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       28.50        40.83        39.16        56.94        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       32.02        18.21        61.68        35.67        27.19        53.95 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        49.05        48.13        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E1 
        3.22         2.56        38.47        67.86        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30        44.81        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G 
       51.32        27.25        24.95        42.35        44.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        7.23        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       30.28        37.55        66.05        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        55.69        49.58        17.69        31.53        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62       114.15        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63        72.07       144.59        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
        8.94         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.16         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.12         4.11        12.33        10.92        11.34        11.28 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.53        12.20         0.03         0.23        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       19.46        13.25        20.58        14.17        13.48        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG 
       14.17        17.49        18.71        15.78        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XL TCGA-D8-A1XM 
       23.90        18.15        12.39        17.16        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.41        16.31         6.35        15.16        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I 
       15.52         9.93        14.24        17.42        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W 
       12.53        12.26        33.37        18.51        21.67         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.10        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14S TCGA-E2-A14T 
       37.51        40.11        28.44        28.87        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 
       43.33        34.26        32.02        31.96        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.24        21.04        23.87        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.19        20.98        11.08        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        28.90         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       15.72         8.28        30.61        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       36.82        13.12        36.56        35.77        25.84        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC 
       28.27        34.95         6.12         3.02         2.76        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       41.03        20.71        17.06        27.22        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO 
       29.72         0.76        18.41        30.18        12.33        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       14.40        15.39        12.20         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        15.68        28.77        29.95        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        29.82        18.48        30.08        18.90        19.99 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        19.96        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       34.03        10.16        23.51        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       75.02        86.96       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.43        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       24.95        10.95        25.05        17.06        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26         2.63        15.68        14.50        14.70        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       14.07        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       26.70        65.62        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01        64.21         0.26 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
       16.50        13.12        16.80        13.84        15.35        13.84 
TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        3.81        11.41        52.96        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           220.90            234.28 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            23.11             24.95 
[1] "0.0 - 220.9 (23.1)" "0.0 - 234.3 (24.9)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        26       17        1        0       124        82
  4P LOSS WILD-TYPE      63       64        7        3       229       163
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           0         52         10         20        7
  4P LOSS WILD-TYPE         2         98         19         43       13
                   vv
clus                STAGE TIS STAGE X
  4P LOSS MUTATED           0       4
  4P LOSS WILD-TYPE         1       9
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 26                63
  STAGE IA                17                64
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA              124               229
  STAGE IIB               82               163
  STAGE III                0                 2
  STAGE IIIA              52                98
  STAGE IIIB              10                19
  STAGE IIIC              20                43
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  4                 9
[1] 13  2
[1] TRUE
[1] "dimension of 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    70 222  38  15
  4P LOSS WILD-TYPE 202 394  92  25
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              70               202
  T2             222               394
  T3              38                92
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED   161 115  44  22
  4P LOSS WILD-TYPE 340 235  73  53
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             161               340
  N1             115               235
  N2              44                73
  N3              22                53
[1] 4 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   293   7
  4P LOSS WILD-TYPE 586  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    293    7
  4P LOSS WILD-TYPE  586   14
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             293               586
  1               7                14
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   343   4
  4P LOSS WILD-TYPE 708   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    343    4
  4P LOSS WILD-TYPE  708    7
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE             343               708
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P LOSS MUTATED                            1                           286
  4P LOSS WILD-TYPE                          0                           477
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P LOSS MUTATED                               32                   3
  4P LOSS WILD-TYPE                            160                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P LOSS MUTATED                       3                                6
  4P LOSS WILD-TYPE                     1                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4P LOSS MUTATED                    0             15
  4P LOSS WILD-TYPE                 17             33
D48V8, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                286               477
  INFILTRATING LOBULAR CARCINOMA                32               160
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          3                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                15                33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    98 249
  4P LOSS WILD-TYPE 190 525
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     98  249
  4P LOSS WILD-TYPE  190  525
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               98               190
  YES             249               525
[1] 2 2
[1] FALSE
D48V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1    20
  4P LOSS WILD-TYPE                                0    40
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          74   227
  4P LOSS WILD-TYPE                        96   509
D48V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         20                40
  BLACK OR AFRICAN AMERICAN                     74                96
  WHITE                                        227               509
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10 286
  4P LOSS WILD-TYPE  28 572
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10  286
  4P LOSS WILD-TYPE   28  572
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                28
  NOT HISPANIC OR LATINO             286               572
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   262  39
  4Q LOSS WILD-TYPE 654  89
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              301               743 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               39                89 
$`4Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO 
      129.14        42.81        20.88        31.79        39.32        28.01 
TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW 
       18.02       101.98        99.12        75.55        98.99       107.93 
TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 
       67.33        79.76        27.12        50.43        17.13        20.75 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XT 
       18.21        18.61        17.36        19.20        17.19        83.01 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       50.37        24.39        35.31        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       25.15        23.74        21.73        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06T 
       14.73        10.29         9.37        10.42         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02        17.03        43.00        19.99 
TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
        8.98        15.06        38.01        33.01        12.00         9.99 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09R 
        0.99        43.00        30.97         1.02        49.05         8.98 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A5XS 
       14.01         2.37        38.53         0.92        32.45         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
       11.44        13.71        17.42        13.58         0.03         1.12 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AR 
        0.23         0.33         0.62         2.96         9.96         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FV 
        0.33         0.33         6.44         7.96         7.00         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT 
        0.36         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD 
        5.59        66.77        32.78        52.18        20.32        72.00 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D 
       76.77        71.80       102.58       108.03        90.58        64.04 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 
       48.36        61.87         0.53        17.79       130.09         5.65 
TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH 
        5.26        55.86        65.36       101.95       114.02        75.55 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       76.11        43.73        43.07        33.73       160.90        50.89 
TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 
       84.20       104.28        97.84        85.35        50.96        78.48 
TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH 
       93.83        10.59        77.62       220.90       129.57       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      176.98        18.77        84.59       110.14       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY 
      189.01        81.17       131.21        79.63        21.47       113.79 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AV 
       43.59        73.51        85.35        68.12       103.63        59.84 
TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF 
       20.45        46.95        39.55        48.36        37.22        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV 
       21.70        44.05        48.69        53.69        45.57        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB 
       41.75        44.02         4.41         9.63        46.19        24.49 
TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX 
       10.78        23.08        20.38        12.89        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A18V 
       23.93        23.05         8.81        55.63        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD 
       69.93        42.28        12.00        97.48        24.66        33.17 
TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 
       72.07        38.60        57.83       130.16        18.64        23.51 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       11.93        11.77         4.08         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A8HR 
        2.30         0.43         9.50         0.99        13.02        13.41 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ 
       11.90        20.88        16.50        18.90        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.12        19.40        21.01        14.73        21.83        14.50 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A27H TCGA-D8-A27T TCGA-D8-A73U 
       15.55        15.85        12.99        13.05        13.08        16.18 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A154 
       47.15        44.68        38.24        38.60        25.41        19.43 
TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH 
       25.05        12.92        14.07        53.62        17.10        33.73 
TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       33.70        27.42        39.62        18.87       106.75       102.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
       34.92        26.56        12.85        13.48        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA 
       12.59        35.24         9.86         2.56         6.12        32.09 
TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 
       32.09        34.13        12.89        23.51         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
        7.13        26.07        15.72        23.84        14.70         0.79 
TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ 
       39.72        18.90        25.94        22.82        29.85        40.41 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR 
       23.11         7.86         6.15        10.52        19.96        55.00 
TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A3XL 
       17.49         7.40        70.85        72.10        85.15        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FR 
        2.60        11.84        11.57        11.44        15.32        16.08 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
        7.46        14.73        58.52        36.36        20.38        41.92 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 
       86.96         0.16        16.93        14.96        13.94        17.03 
TCGA-WT-AB44 
       29.03 

$`4Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68         7.96        19.20        18.21       104.81        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        87.25        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25         5.19        56.81        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72       134.40        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       63.29        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
        8.38        49.84        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        31.73        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        49.48        47.31        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       38.30        34.29        35.47        37.45        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       20.19        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A5ZV 
       13.41        14.70        11.97        14.93        13.74        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       10.72        11.05         8.75        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       29.03        53.98         9.01        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        18.05        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       28.96        19.96        37.05        31.00        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
      112.08        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99        12.00        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         5.72         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70        33.04         2.27        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV 
       14.99        16.57        19.79        23.24        24.79        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.33         1.78         1.71         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        0.16         5.65         7.59         7.17         6.28         7.04 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XU 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.33        80.28        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF 
       22.36        53.03        21.53        50.70        50.86        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        55.33        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      106.78        98.27        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       82.62        70.39        24.79        26.93        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        32.91        19.20       111.32        73.64        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
       86.66        42.35        98.93        64.83       107.24        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
       85.97        61.84        52.77        51.25        48.82        43.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R 
       62.14        94.22        96.89        78.51         2.76        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       76.01        53.36        83.77        79.00        89.00        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        58.92       143.21        20.25        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       54.74        16.04        20.45       143.38       149.59        12.13 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       50.70        65.72       146.50       126.12       110.93        68.45 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       157.41        97.48       188.68        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AU 
      101.52       139.17       170.17        74.99        71.15        24.53 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       25.55        28.50        40.83        39.16        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO 
       51.68        32.02        18.21        24.85        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       27.19        53.95        11.67        49.05        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       67.86        47.41        16.27        15.68        14.30        44.81 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        31.00        24.43        30.35        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK 
       35.51        24.56        41.00        52.96        26.50         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 
        2.50        13.61        36.85        51.32        27.25        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       42.35        44.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX 
        7.36        91.99       113.82        82.85        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
       17.69        25.81        31.53        89.16       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O 
       72.07       144.59        28.14        26.14        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 
        6.44        20.12        10.52       109.28         8.94         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        5.26         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.05         4.11        12.33        10.92        11.34        11.28 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        9.53         0.03        12.20         0.03         0.23        12.49 
TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       19.46        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        14.17        17.49        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN 
       18.15        12.03        14.01        18.97        20.09        20.38 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT 
       15.22        19.92        17.69        16.41        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I 
       14.24        14.14        17.42        16.04        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W 
       12.53        12.26        33.37        18.51        21.67         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.10        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14S 
       37.51        40.11        28.44        28.87        40.96        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       18.51        27.12        23.24        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58        11.05        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        60.53        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        38.30        37.41        32.78 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK 
       54.18        19.66        24.59        40.47        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         8.28        30.61 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.29        34.82        32.88        36.82        13.12        36.56 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 
       35.77        25.84        11.90        28.27        34.95         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        21.21        40.24         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        34.59        35.64        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       39.09        22.75        41.03        20.71        17.06        27.22 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56         0.72        29.72         0.76        18.41        30.18 
TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY 
       12.33        13.81        14.40        15.39        12.20         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX 
       18.21        13.25        16.57        15.68        28.77        29.95 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS 
       18.90        19.99        13.94        14.43        34.55        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 
       25.91        22.09        34.03        10.16        23.51       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DK 
       59.57       216.76        79.10        83.34        75.02        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.43 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95        25.05        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26         2.63        15.68        14.50        14.70        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       14.07        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        23.47        65.62        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z 
       64.21         0.26         9.93        16.50        13.12        16.80 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-UU-A93S TCGA-W8-A86G 
       15.39        13.84        15.35        13.84         3.81        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        15.35        16.04       108.07       107.05 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.03              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           220.90            234.28 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            23.51             24.79 
[1] "0.0 - 220.9 (23.5)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        22       18        0        0       107        70
  4Q LOSS WILD-TYPE      67       63        8        3       246       175
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           0         49          9         17        7
  4Q LOSS WILD-TYPE         2        101         20         46       13
                   vv
clus                STAGE TIS STAGE X
  4Q LOSS MUTATED           0       5
  4Q LOSS WILD-TYPE         1       8
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 22                67
  STAGE IA                18                63
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA              107               246
  STAGE IIB               70               175
  STAGE III                0                 2
  STAGE IIIA              49               101
  STAGE IIIB               9                20
  STAGE IIIC              17                46
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    61 190  39  15
  4Q LOSS WILD-TYPE 211 426  91  25
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              61               211
  T2             190               426
  T3              39                91
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED   141 101  39  20
  4Q LOSS WILD-TYPE 360 249  78  55
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             141               360
  N1             101               249
  N2              39                78
  N3              20                55
[1] 4 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   259   7
  4Q LOSS WILD-TYPE 620  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    259    7
  4Q LOSS WILD-TYPE  620   14
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             259               620
  1               7                14
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   305   2
  4Q LOSS WILD-TYPE 746   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    305    2
  4Q LOSS WILD-TYPE  746    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE             305               746
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q LOSS MUTATED                            0                           250
  4Q LOSS WILD-TYPE                          1                           513
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q LOSS MUTATED                               30                   2
  4Q LOSS WILD-TYPE                            162                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q LOSS MUTATED                       3                                6
  4Q LOSS WILD-TYPE                     1                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4Q LOSS MUTATED                    0             15
  4Q LOSS WILD-TYPE                 17             33
D49V8, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                250               513
  INFILTRATING LOBULAR CARCINOMA                30               162
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                15                33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    90 217
  4Q LOSS WILD-TYPE 198 557
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     90  217
  4Q LOSS WILD-TYPE  198  557
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               90               198
  YES             217               557
[1] 2 2
[1] FALSE
D49V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1    18
  4Q LOSS WILD-TYPE                                0    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          64   198
  4Q LOSS WILD-TYPE                       106   538
D49V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     64               106
  WHITE                                        198               538
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9 245
  4Q LOSS WILD-TYPE  29 613
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9  245
  4Q LOSS WILD-TYPE   29  613
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                29
  NOT HISPANIC OR LATINO             245               613
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED   113  22
  5P LOSS WILD-TYPE 803 106
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              135               909 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               22               106 
$`5P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
        9.96        31.79        28.01        18.02        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ 
       24.79        67.33        63.29        50.43        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        83.01        47.31        34.98 
TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A6VY TCGA-A8-A06T 
       35.67        20.19        21.73        21.17         8.75        53.06 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08X 
       17.03        53.98         9.99         8.98        15.06        43.00 
TCGA-AC-A2BK TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
       38.53        13.58         0.23         7.36         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A0J4 TCGA-AO-A0J5 
        0.33         7.59         7.04         0.33        52.18        26.04 
TCGA-AO-A0JB TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A04L 
       50.70       102.58       108.03        48.36        26.93       130.09 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
       65.36        83.87        75.55        52.77        43.07        17.23 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB 
       50.89       104.28        97.84        89.00        78.48       129.57 
TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A402 TCGA-BH-A0B4 
      146.50       110.14       102.77       131.21        74.99        39.16 
TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0WA 
       24.85        45.57        41.75         4.41        52.96        23.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU 
        7.36        51.16       114.15        74.73        72.07        72.07 
TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A26W 
      130.16        12.66         1.12         4.08        10.92         0.23 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A9FZ TCGA-D8-A147 TCGA-D8-A1JB 
        0.36         9.50        12.20        19.46        19.20        18.71 
TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XZ 
       12.03        15.22        21.83        14.50        16.41        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27R TCGA-E2-A14N TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ 
       14.14        10.09        47.15        25.05        23.34        60.53 
TCGA-E2-A1B6 TCGA-E2-A1L7 TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 
       28.50        27.42       102.61         8.75        43.04        34.92 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A22D TCGA-E9-A22G 
       12.00        39.55        12.59        35.24        41.03        23.51 
TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P8 
        0.69        30.18        22.82        29.85        41.13         7.86 
TCGA-EW-A2FV TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       25.91        75.02        70.85        69.30         2.60        11.84 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A66J 
        7.10        11.44        58.52        36.36        23.47        65.62 
TCGA-OL-A6VO TCGA-S3-AA10 TCGA-WT-AB41 
       28.21        15.39        52.96 

$`5P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
       18.21       104.81        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       20.88        39.65        29.98        32.75        49.48        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F 
       30.61        37.45        33.11        29.79        31.73        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42        13.02        13.02         1.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       29.03        31.00        26.01         1.02         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99        24.99         9.99        45.07        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       17.42        18.67        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
       20.19         1.12         1.32         2.30         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.16         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.17         6.28         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        32.78        21.40        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        50.24        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       106.78        90.58        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
        0.53        17.79        24.79         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        42.35        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK 
      107.24       101.95       114.02        85.97        61.84        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
       48.82        76.11        43.73        43.56        39.98        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22        96.89        78.51        84.20         2.76        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       220.90        50.70 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       162.05       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        68.12       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       35.67        48.69        27.19        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        7.23        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        55.63        37.55        66.05        51.39        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66       120.62        33.17       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        45.63       144.59        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31        57.83        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 
       12.66         0.39         3.16         2.24         1.87         1.05 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11        12.33        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42         2.30         3.25         0.30         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         9.53         0.03         0.99         0.03         0.23 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       13.02        12.49        13.41        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       20.58        13.97        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       17.49        16.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       12.39        17.16        14.73        19.92        17.69        15.55 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       16.54        15.52         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        18.51        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        14.79        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC 
       14.99        53.62        53.03        33.01        32.35        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       18.87       106.75        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        26.56        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        13.48        13.12        36.56        35.77        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       12.89        20.71        17.06        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       15.72        12.33        23.84        14.70         0.79        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.95        40.41        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        34.03        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DH 
      109.87        59.57       216.76        79.10        83.34        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        62.43        11.57        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       10.62        24.95        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       15.68         7.46        14.50        14.70        12.36        14.73 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       14.07        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       20.38        26.70        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.93        16.80        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB44 TCGA-XX-A899 
       13.94        17.03         3.81        11.41        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.23              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           146.50            234.28 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            28.21             23.84 
[1] "0.2 - 146.5 (28.2)" "0.0 - 234.3 (23.8)"
[1] "hr=" "1.2"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         9        7        0        0        55        32
  5P LOSS WILD-TYPE      80       74        8        3       298       213
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           0         19          3         10        2
  5P LOSS WILD-TYPE         2        131         26         53       18
                   vv
clus                STAGE TIS STAGE X
  5P LOSS MUTATED           0       0
  5P LOSS WILD-TYPE         1      13
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 7                74
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               55               298
  STAGE IIB               32               213
  STAGE III                0                 2
  STAGE IIIA              19               131
  STAGE IIIB               3                26
  STAGE IIIC              10                53
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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    27  97   9   5
  5P LOSS WILD-TYPE 245 519 121  35
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              27               245
  T2              97               519
  T3               9               121
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    67  43  16  11
  5P LOSS WILD-TYPE 434 307 101  64
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              67               434
  N1              43               307
  N2              16               101
  N3              11                64
[1] 4 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   115   2
  5P LOSS WILD-TYPE 764  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    115    2
  5P LOSS WILD-TYPE  764   19
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0             115               764
  1               2                19
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   137   1
  5P LOSS WILD-TYPE 914  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    137    1
  5P LOSS WILD-TYPE  914   10
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE             137               914
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P LOSS MUTATED                            0                           118
  5P LOSS WILD-TYPE                          1                           645
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P LOSS MUTATED                                2                   4
  5P LOSS WILD-TYPE                            190                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P LOSS MUTATED                       0                                5
  5P LOSS WILD-TYPE                     4                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5P LOSS MUTATED                    0              8
  5P LOSS WILD-TYPE                 17             40
D50V8, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                118               645
  INFILTRATING LOBULAR CARCINOMA                 2               190
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                25
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    43  95
  5P LOSS WILD-TYPE 245 679
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     43   95
  5P LOSS WILD-TYPE  245  679
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               43               245
  YES              95               679
[1] 2 2
[1] FALSE
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0    11
  5P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          31    87
  5P LOSS WILD-TYPE                       139   649
D50V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     31               139
  WHITE                                         87               649
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3 116
  5P LOSS WILD-TYPE  35 742
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3  116
  5P LOSS WILD-TYPE   35  742
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                35
  NOT HISPANIC OR LATINO             116               742
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   189  29
  5Q LOSS WILD-TYPE 727  99
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              218               826 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               29                99 
$`5Q LOSS MUTATED`
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      131.67         9.96        31.79        28.01        19.20        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0D0 
       78.41        73.84        87.25       101.98        24.79        67.33 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ 
       34.55        79.76        63.29        50.43        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        83.01        47.31        34.98 
TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
        7.30        21.90        30.61        35.67        31.73        20.19 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       23.74        21.73        21.17        17.92        14.73        12.10 
TCGA-A7-A6VY TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R 
        8.75        31.00        17.03        53.98         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09K 
       24.99        15.06        33.01        43.00         9.99        29.98 
TCGA-AC-A2BK TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04C 
       38.53        13.71        13.58         1.12         0.23         1.78 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL 
        7.36         6.51         0.33         0.33         7.96         7.59 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XU 
        7.04         0.33         0.33         0.33         0.33         0.33 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 
       52.18        26.04        50.70        55.33       102.58       108.03 
TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP 
       48.36        70.39        26.93       130.09         2.56       111.32 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ 
       86.66        42.35        65.36        83.87        75.55        52.77 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S 
       43.07        17.23        33.73        50.89       104.28        97.84 
TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE 
       53.36        79.00        89.00        78.48       129.57        65.72 
TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU 
      146.50       110.14       211.56       102.77       100.70       131.21 
TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BF 
       21.47       101.52        74.99        59.84        39.55        25.71 
TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 
       24.85        48.69        45.57        11.67        41.75         4.41 
TCGA-BH-A0E6 TCGA-BH-A0HA TCGA-BH-A0WA TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EV 
        9.63        52.96        23.05         7.36        51.16        12.00 
TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 
       31.53       114.15        74.73        72.07        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A130 TCGA-C8-A131 
      130.16        18.64        11.93        12.66         3.16         2.24 
TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W 
        1.12         4.08        10.92         0.16         2.30         0.23 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.36         9.50        12.20         0.99        13.41        19.46 
TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL 
       13.97        19.20        18.71        12.03        20.12        20.09 
TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW 
       15.22        14.50        19.92        16.41         6.35        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27R 
       15.32        14.14        16.04        13.05        13.48        10.09 
TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 
       40.11        47.15        25.41        21.04        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1IO 
       23.34        60.53        53.62        28.50        33.70        20.98 
TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 
       27.42        24.59       102.61         8.75        43.04        34.92 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH 
       26.56        12.00        39.55        12.59        32.09        34.59 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P0 
       41.03        23.51         0.69        30.18        22.82        41.13 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PH TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DD 
        7.86        18.90        19.96        25.91       109.87        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A7W5 
       70.85        72.10        69.30         2.60        11.84         7.10 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5D7 
       11.44        15.32        14.70        14.79        16.08        58.52 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-PL-A8LX 
       36.36        22.32        20.38        23.47        65.62         0.16 
TCGA-S3-AA10 TCGA-WT-AB41 
       15.39        52.96 

$`5Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68         7.96        39.32        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        63.12        55.43        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        98.99       107.93        56.81        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72       134.40        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       20.88        39.65        29.98        32.75        49.48        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37        24.39        21.30        23.21        26.96        21.14 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.50        10.72        11.05        10.29         9.37        10.42 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S 
       18.97        14.01        12.00        32.05        10.98         7.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        18.05        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       38.01        28.96        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
       31.00        31.00         0.99        33.01       112.08        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M 
       12.00         1.02        50.04        49.05        45.07        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       18.67        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD 
        2.96         1.71         9.96         0.16         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX 
        5.65         7.00         7.17         6.28         0.36         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       62.04        71.80        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        64.04        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 
       82.62        61.87         0.53        17.79        24.79         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52        32.91        19.20        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       74.79        98.93        64.83        55.86       107.24       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        61.84        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.73        43.56        39.98        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
       84.20         2.76        87.22        76.01        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       83.77        73.18        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.93       140.88        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       172.96       162.05       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        79.63        18.35       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        24.53        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       37.22        32.02        18.21        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ 
       35.67        27.19        53.69        53.95        49.94        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        47.41        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        23.08        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       44.81         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       42.28        55.69        49.58        17.69        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48        24.66       120.62        33.17       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       63.35        55.00        45.63       144.59        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        83.31        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28         8.94        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P 
       18.87        21.76         9.44        11.77        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.87         1.05         4.11        12.33        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z 
       12.03        10.42         3.25         0.30         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.67         9.53         0.03         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       12.49        11.90        20.88        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.48        21.14        14.17        17.49        16.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM 
       18.15        12.39        17.16        14.73        21.83        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY 
       15.55        15.85        16.31        12.99        15.16        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I 
       15.52         9.93        14.24        17.42        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
        9.44        16.41         4.80         0.76        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.10        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        18.51        27.12        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.87        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 
       13.02        19.56        17.06        14.07        14.99        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        28.44        22.65         3.88        22.19 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        39.62        19.66        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       18.87       106.75        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.29        12.85        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       13.48        13.12        36.56        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02         2.76        21.21        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        21.27        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       29.72         0.76        26.07        18.41        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        23.51         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       83.34        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        62.43        11.57        21.24        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        10.95        25.05        17.06 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.47        22.26         2.63        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       28.87        24.72        26.70        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       47.01        64.21        86.96         0.26         9.93        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       13.12        16.93        16.80        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB44 
       13.84        13.94        17.03         3.81        11.41        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.16              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           211.56            234.28 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.69             24.51 
[1] "0.2 - 211.6 (24.7)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       10        1        0        92        52
  5Q LOSS WILD-TYPE      73       71        7        3       261       193
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           0         26          5         12        4
  5Q LOSS WILD-TYPE         2        124         24         51       16
                   vv
clus                STAGE TIS STAGE X
  5Q LOSS MUTATED           1       2
  5Q LOSS WILD-TYPE         0      11
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 16                73
  STAGE IA                10                71
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               92               261
  STAGE IIB               52               193
  STAGE III                0                 2
  STAGE IIIA              26               124
  STAGE IIIB               5                24
  STAGE IIIC              12                51
  STAGE IV                 4                16
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    44 153  15   8
  5Q LOSS WILD-TYPE 228 463 115  32
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              44               228
  T2             153               463
  T3              15               115
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED   114  68  24  13
  5Q LOSS WILD-TYPE 387 282  93  62
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             114               387
  N1              68               282
  N2              24                93
  N3              13                62
[1] 4 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   192   4
  5Q LOSS WILD-TYPE 687  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    192    4
  5Q LOSS WILD-TYPE  687   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             192               687
  1               4                17
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   222   0
  5Q LOSS WILD-TYPE 829  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    222    0
  5Q LOSS WILD-TYPE  829   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE             222               829
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q LOSS MUTATED                            1                           197
  5Q LOSS WILD-TYPE                          0                           566
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q LOSS MUTATED                                4                   4
  5Q LOSS WILD-TYPE                            188                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q LOSS MUTATED                       0                                5
  5Q LOSS WILD-TYPE                     4                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5Q LOSS MUTATED                    0             10
  5Q LOSS WILD-TYPE                 17             38
D51V8, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                197               566
  INFILTRATING LOBULAR CARCINOMA                 4               188
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                25
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                10                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    64 158
  5Q LOSS WILD-TYPE 224 616
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     64  158
  5Q LOSS WILD-TYPE  224  616
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               64               224
  YES             158               616
[1] 2 2
[1] FALSE
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0    18
  5Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          57   130
  5Q LOSS WILD-TYPE                       113   606
D51V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     57               113
  WHITE                                        130               606
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 185
  5Q LOSS WILD-TYPE  33 673
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  185
  5Q LOSS WILD-TYPE   33  673
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                33
  NOT HISPANIC OR LATINO             185               673
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   162  19
  6P LOSS WILD-TYPE 754 109
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              181               863 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19               109 
$`6P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SP TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W 
      129.14        42.81        19.20       121.94        87.25       101.98 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 
       25.22        80.28        27.12        49.84        20.52        20.75 
TCGA-A2-A1FW TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A2KD 
       17.36        39.65        49.48        21.30        31.73        22.32 
TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S 
       13.02        26.01         1.02         9.01        12.00         7.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09C 
       33.01        19.96        12.00        31.00        12.00         1.02 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 
       29.98        33.07         1.02         8.98        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM 
       21.04        27.02        17.03        10.85        38.53        99.35 
TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A04C 
       26.04        32.45        17.42        20.19         1.32         1.78 
TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03T TCGA-AO-A0J6 
        5.65         0.33         0.33         5.59        47.87        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A1KR TCGA-AO-A1KT 
       20.32        22.36        26.24        62.04        70.39        17.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A24K 
        2.56        32.91        73.64        39.98        76.21        50.89 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 TCGA-B6-A0IA TCGA-B6-A0IJ 
        2.76        87.22        85.35        73.18       220.90       176.98 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 
      162.05        79.63        85.35        24.53        46.95        48.36 
TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 TCGA-BH-A0EI 
       48.69        48.13        48.23        15.65        14.30        24.43 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18I 
       23.08        52.96        51.32        27.25        23.93         7.23 
TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EY TCGA-BH-A1F5 
       26.66        66.05       113.82        42.28        17.69        89.16 
TCGA-BH-A1FE TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12O 
       74.73        63.35        45.63        23.51        18.87        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A274 TCGA-C8-A27A 
       11.77        12.66         4.11        11.34         9.53        12.20 
TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JE 
       13.02        13.41        19.46        13.48        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1Y1 
       12.03        19.40        27.58        15.22        12.99         9.93 
TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14V TCGA-E2-A152 
       12.26         8.02        34.42        46.59        34.26        27.12 
TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15R TCGA-E2-A1AZ 
       23.24        20.71        21.63        12.92        17.06        60.53 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A9RU 
       17.10        38.30        39.62        28.90        43.04        12.85 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1QZ 
       13.48        12.00        36.56        35.77        35.24        11.90 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RI 
        6.12         2.76        32.09        32.09        21.27        35.64 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS TCGA-E9-A3X8 
       13.32        39.09         1.94         7.13        29.72        15.72 
TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-GM-A2DB TCGA-GM-A2DC 
       14.40        18.90        28.77        23.11        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U 
       75.02        69.30        15.32        14.70        14.73        22.39 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA14 
       28.21        19.73        40.11        13.12        16.93        14.96 
TCGA-UU-A93S 
        3.81 

$`6P LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V 
       18.21       104.81        18.02        78.41        73.84        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       92.48       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       61.58       101.72       134.40       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.52        17.13         8.38        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        33.93        83.01        29.98        32.75 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        34.98        50.37        38.37         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        32.05         9.99        10.98         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L 
       13.02         0.99        38.01        28.96        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09V 
       12.00        50.04        49.05        45.07        25.02        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD 
        0.99        14.01        12.00        19.04         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95         2.37         5.72         1.48        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        50.70        33.04         0.92         2.27 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        13.71        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ 
       13.58        12.26         1.68         8.22         0.03         1.12 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.71         9.96         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         0.33         6.44         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY 
        7.59         7.17         6.28         7.04         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        95.70        68.75        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA 
       32.78        21.40        52.18        26.04        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI 
       50.70        50.86        72.00        76.77        21.37        50.24 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        61.87         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       111.32         5.26        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       51.25        48.82        76.11        43.73        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        61.28        63.62        62.14        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q 
      160.90        94.22        96.89        78.51        84.20       104.28 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84        76.01        53.36        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        78.48        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB 
       10.59        77.62       143.38       149.59        12.13       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      189.01       234.28        81.17        78.02       172.96       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        18.35        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        74.99        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 
       71.15        59.84        20.45        25.55        28.50        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        35.67        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       49.94        11.67        49.05        41.75        44.02        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        24.49        31.00        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       37.78        35.51        24.56        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        12.89        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
        5.59        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        2.01        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       55.63        37.55         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       91.99        82.85        12.00        55.69        49.58        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        24.66       120.62       114.15        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
      122.89        36.92        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       28.14        26.14        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 
       18.64         9.63         5.26         9.70        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
        1.05         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
        0.36         0.43         8.28         9.67         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z 
        0.99         0.03         0.23        12.49        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        13.97        14.17        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       14.17        17.49        16.50        18.71        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       14.01        18.97        20.09        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31         6.35        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        15.52        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A105 
       33.37        18.51        21.67        16.18        12.10        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.30        43.33        32.02        31.96        28.60        18.51 
TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       25.41        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       23.34        22.82        17.29        18.21        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
        9.04        20.58        11.05        13.02        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       27.42        19.66        24.59        40.47        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        26.56        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1NI 
       36.82        13.12        39.55        12.59        25.84         9.86 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC 
       28.27        34.95         2.56         3.02        21.21        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
        1.12        34.65         6.58        34.59        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       12.53        22.75        41.03        12.89        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       17.06         0.69        27.22        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41        30.18        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        13.81        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        13.25        16.57        15.68        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        11.44        10.95        25.05        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        7.46        14.50        12.36        14.07        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       14.07         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        16.50        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 
       15.35        13.84        13.94        17.03        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.33              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           220.90            234.28 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            23.24             24.72 
[1] "0.3 - 220.9 (23.2)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED        15       16        1        0        63        43
  6P LOSS WILD-TYPE      74       65        7        3       290       202
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           0         25          6          8        4
  6P LOSS WILD-TYPE         2        125         23         55       16
                   vv
clus                STAGE TIS STAGE X
  6P LOSS MUTATED           0       3
  6P LOSS WILD-TYPE         1      10
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 15                74
  STAGE IA                16                65
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               63               290
  STAGE IIB               43               202
  STAGE III                0                 2
  STAGE IIIA              25               125
  STAGE IIIB               6                23
  STAGE IIIC               8                55
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of 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    52 106  17   8
  6P LOSS WILD-TYPE 220 510 113  32
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              52               220
  T2             106               510
  T3              17               113
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    87  63  20  12
  6P LOSS WILD-TYPE 414 287  97  63
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              87               414
  N1              63               287
  N2              20                97
  N3              12                63
[1] 4 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   157   4
  6P LOSS WILD-TYPE 722  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    157    4
  6P LOSS WILD-TYPE  722   17
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0             157               722
  1               4                17
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   183   1
  6P LOSS WILD-TYPE 868  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    183    1
  6P LOSS WILD-TYPE  868   10
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE             183               868
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P LOSS MUTATED                            0                           140
  6P LOSS WILD-TYPE                          1                           623
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P LOSS MUTATED                               24                   1
  6P LOSS WILD-TYPE                            168                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P LOSS MUTATED                       1                                7
  6P LOSS WILD-TYPE                     3                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6P LOSS MUTATED                    5              6
  6P LOSS WILD-TYPE                 12             42
D52V8, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                140               623
  INFILTRATING LOBULAR CARCINOMA                24               168
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             5                12
  OTHER  SPECIFY                                 6                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    56 128
  6P LOSS WILD-TYPE 232 646
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     56  128
  6P LOSS WILD-TYPE  232  646
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               56               232
  YES             128               646
[1] 2 2
[1] FALSE
D52V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0    13
  6P LOSS WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          32   116
  6P LOSS WILD-TYPE                       138   620
D52V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     32               138
  WHITE                                        116               620
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     4 147
  6P LOSS WILD-TYPE  34 711
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4  147
  6P LOSS WILD-TYPE   34  711
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO             147               711
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   239  28
  6Q LOSS WILD-TYPE 677 100
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              267               777 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28               100 
$`6Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SN 
      129.14       131.67        42.81         9.96        43.43        39.32 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CQ TCGA-A2-A0CR 
      121.94        73.84        87.25       101.98        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D4 TCGA-A2-A0EO 
       75.55        75.25         5.19        98.99        25.22        80.28 
TCGA-A2-A0ET TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       35.05        27.12        49.84        20.52        18.90        20.75 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KD 
       23.77        17.36       107.70        42.44       105.34        39.65 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A13F 
       33.93        32.75        49.48        21.30        31.73        25.15 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A8-A06O TCGA-A8-A06Y 
       20.61        11.34        11.28        11.97        13.02        26.01 
TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08F 
        1.02        53.98         9.01        12.00         7.99        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09A 
       19.96        12.00        37.05        31.00        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
        8.98        19.04        13.02        21.04        27.02        17.03 
TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3W5 
       10.85        38.53        99.35        26.04        32.45        16.57 
TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AS 
       17.42        20.19         1.32         0.23         1.78         0.33 
TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03R 
        5.65         0.33         0.33         5.59        66.77        68.75 
TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG 
       47.87        21.40        37.48        20.32        22.36        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A54N 
       50.24        62.04        55.33        70.39        17.79         2.56 
TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AU 
       32.91        73.64         5.26       107.24        83.87        76.21 
TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 TCGA-AR-A255 
       50.89         2.76        87.22        85.35        73.18        58.92 
TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RG TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV 
      220.90       176.98        68.45       162.05       131.21        79.63 
TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
      113.79        43.59       139.17       170.17        85.35        68.12 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BJ TCGA-BH-A0BM 
       71.15        24.53        46.95        48.36        21.70        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DH 
       48.69        27.19        11.67        48.13        31.17        38.01 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 
       48.23        15.65        14.30        24.43        15.16        23.08 
TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18I 
       52.96        51.32        27.25        23.93         8.81         7.23 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU 
       90.84        26.66        66.05        69.93       113.82        42.28 
TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A201 
       89.16       114.15        74.73        63.35        45.63        28.14 
TCGA-BH-A8FZ TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 
       18.87        11.77        12.66        11.77        12.66         4.11 
TCGA-C8-A1HG TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HR 
       11.34         0.43         9.67        12.20        13.02        13.41 
TCGA-C8-A9FZ TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       19.46        13.48        18.71        18.15        18.90        12.03 
TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       18.97        19.40        27.58        18.15        15.22        19.92 
TCGA-D8-A1XM TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27R 
       17.69         6.35        12.99        15.52         9.93        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10F 
       13.08        12.26         8.02        34.42        46.59        28.87 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       34.26        27.12        23.24        20.71        21.63        12.92 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       19.56        17.06        60.53        16.47        17.10        38.30 
TCGA-E2-A1IL TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A9RU 
        3.88        39.62        28.90        18.87        43.04        12.85 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE 
       32.88        36.82        13.48        12.00        36.56        35.77 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
       11.90        28.27         6.12         2.76        32.09        32.09 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 
       21.27        34.59        35.64        13.32        39.09         1.94 
TCGA-E9-A249 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J1 
        7.13        29.72        15.72        13.81        14.40        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 
       13.25        15.68        28.77        29.85        41.13        23.11 
TCGA-EW-A3E8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL 
       34.03        79.10        83.34        75.02        70.85        69.30 
TCGA-GM-A3XN TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A740 
       66.38        21.24        13.28        10.62        15.32        14.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO 
       14.70        14.73        22.39        42.77        17.36        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       19.73        40.11        47.01        16.50        13.12        16.93 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-UU-A93S 
       15.35        14.96         3.81 

$`6Q LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD 
       40.14        11.44        48.56        48.36         8.52        14.37 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK 
       48.10        14.27        47.24        20.88        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       78.41        63.12        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       24.79       114.81        92.48       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       34.55        33.76        61.58       101.72       134.40       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       79.76        74.40        72.00        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0YC 
       44.28        17.52        17.13         8.38        17.46        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        31.73        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XT TCGA-A2-A3XU 
       17.19        18.15        10.59        20.88        83.01        29.98 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        34.98        50.37        38.37         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        20.19        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        21.73        22.32        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       13.41        14.70        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       53.06        29.03        31.00        17.03        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        14.01        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        8.98        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L 
       36.95        13.02         0.99        38.01        28.96         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B 
       33.01        30.97        17.95        41.98         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       50.04        25.02        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
       19.04         0.99        38.04         0.95         2.37         5.72 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
        1.48        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       33.04         0.92         2.27        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       14.99        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       13.71        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        0.03         1.12         2.30         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.16         0.33         0.33         6.44         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY 
        7.59         7.17         6.28         7.04         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        61.35 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       81.63        95.70        58.95        29.13        32.78        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       26.04        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       76.77        21.37        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       32.52        19.20       111.32        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       98.93        64.83        55.86        65.36       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       76.11        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        61.28        63.62        62.14        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S 
       94.22        96.89        78.51        84.20       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       76.01        53.36        50.96        83.77        79.00        89.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       78.48        72.76        93.83       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59        12.13       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.93       140.88       211.56       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       172.96       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
      157.41        97.48       188.68        18.35        21.47       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       73.51        74.99       103.63        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       28.50        40.83        39.55        39.16        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       44.05        35.67        53.69        53.95        45.57        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG 
       49.05        41.75        44.02        42.90        45.83        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       22.13        13.91        17.26         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 
       67.86        47.41        16.27         4.41        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY 
       44.81        46.19        32.58        24.49        31.00        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB 
       10.78        37.78        35.51        24.56        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
        2.01        20.12        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55         7.36        51.39        51.16        91.99        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48        24.66       120.62        33.17       122.89        36.92 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07       144.59        72.07        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28         8.94        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        5.26         9.70        21.76         9.44        11.93        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
        2.24         1.87         1.12         1.05         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 
        3.25         0.30         0.23         0.36         8.28         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        0.03         9.50         0.99         0.03         0.23        12.49 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       21.14        19.20        14.17        17.49        16.50        15.78 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       12.03        14.01        20.09        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       16.73        25.74        23.90        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        14.50        15.55        16.41        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        12.66        16.54        15.32        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A3Z5 
       16.41        13.48         4.80         0.76        12.53        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 
       18.51        21.67        16.18        12.10        43.00        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        40.11        28.44        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 
       32.02        31.96        28.60        18.51        25.41        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       17.29        18.21        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       11.05        13.02        14.07        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       33.01        32.35        28.50        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        22.65        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       54.18        27.42        19.66        24.59        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N9 
       30.61        34.92        26.56        34.29        34.82        13.12 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 
       39.55        12.59        35.24        25.84         9.86        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.56         3.02        21.21        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D 
        6.58        34.13        32.05        12.53        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       12.89        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56         0.72         0.76        26.07        18.41        30.18 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        23.84        14.70         0.79        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       39.72         8.48        18.21        16.57        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       29.95        40.41        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       25.91        22.09        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      109.87        59.57       216.76        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       43.73        72.03        13.55        18.12         2.60        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A440 TCGA-LL-A441 
       11.84        11.57        13.22         7.10        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95        25.05        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 
       22.26         2.63        16.08        15.68         7.46        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.07        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       26.04        14.07         8.91        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 
        0.26         9.93        16.80        15.39        13.84        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       13.94        17.03        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           220.90            234.28 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            25.15             24.49 
[1] "0.2 - 220.9 (25.1)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED        20       25        1        0        88        69
  6Q LOSS WILD-TYPE      69       56        7        3       265       176
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           0         37          9         13        5
  6Q LOSS WILD-TYPE         2        113         20         50       15
                   vv
clus                STAGE TIS STAGE X
  6Q LOSS MUTATED           0       4
  6Q LOSS WILD-TYPE         1       9
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 20                69
  STAGE IA                25                56
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               88               265
  STAGE IIB               69               176
  STAGE III                0                 2
  STAGE IIIA              37               113
  STAGE IIIB               9                20
  STAGE IIIC              13                50
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  4                 9
[1] 13  2
[1] TRUE
[1] "dimension of 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    78 153  27  12
  6Q LOSS WILD-TYPE 194 463 103  28
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              78               194
  T2             153               463
  T3              27               103
  T4              12                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED   120  98  30  18
  6Q LOSS WILD-TYPE 381 252  87  57
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0             120               381
  N1              98               252
  N2              30                87
  N3              18                57
[1] 4 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   226   6
  6Q LOSS WILD-TYPE 653  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    226    6
  6Q LOSS WILD-TYPE  653   15
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             226               653
  1               6                15
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   270   1
  6Q LOSS WILD-TYPE 781  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    270    1
  6Q LOSS WILD-TYPE  781   10
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             270               781
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q LOSS MUTATED                            0                           199
  6Q LOSS WILD-TYPE                          1                           564
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q LOSS MUTATED                               42                   2
  6Q LOSS WILD-TYPE                            150                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q LOSS MUTATED                       1                               11
  6Q LOSS WILD-TYPE                     3                               19
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6Q LOSS MUTATED                    7              9
  6Q LOSS WILD-TYPE                 10             39
D53V8, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                199               564
  INFILTRATING LOBULAR CARCINOMA                42               150
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)              11                19
  MUCINOUS CARCINOMA                             7                10
  OTHER  SPECIFY                                 9                39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    87 184
  6Q LOSS WILD-TYPE 201 590
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     87  184
  6Q LOSS WILD-TYPE  201  590
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               87               201
  YES             184               590
[1] 2 2
[1] FALSE
D53V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0    16
  6Q LOSS WILD-TYPE                                1    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          49   178
  6Q LOSS WILD-TYPE                       121   558
D53V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     49               121
  WHITE                                        178               558
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     7 220
  6Q LOSS WILD-TYPE  31 638
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7  220
  6Q LOSS WILD-TYPE   31  638
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                31
  NOT HISPANIC OR LATINO             220               638
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    94  13
  7P LOSS WILD-TYPE 822 115
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              107               937 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               115 
$`7P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0D4 
        9.96        31.79        28.01        73.84        75.25        25.22 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW 
       79.76        35.05        50.43        49.84        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A4RX TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC 
       19.20        24.39        21.90        38.30        30.61        29.79 
TCGA-A7-A26I TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 
       21.73        10.42        13.02        29.03        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08L 
       43.00        18.97         8.98        38.01        33.01         9.99 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A09Q TCGA-A8-A0A2 TCGA-A8-A0A9 
       33.01        33.01        30.97        25.02        19.04        27.02 
TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS 
        2.37        33.04        13.71         1.78         0.16         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A12F 
        0.33         0.33         0.33        80.28        20.32        48.36 
TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A255 
        0.53         2.56        85.97        61.84        43.07        58.92 
TCGA-AR-A2LK TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WY 
       54.21       176.98       110.14        68.45       100.70       113.79 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0HI TCGA-BH-A18F 
       74.99        68.12        24.85        41.75        20.38         8.81 
TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1F8 TCGA-BH-A42T TCGA-C8-A1HF 
       26.66        55.63        51.39        24.66        10.52        10.92 
TCGA-C8-A1HM TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JM 
        2.30         9.53        19.20        17.49        18.90        19.40 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ 
       14.70        18.58        27.58        18.15        14.50        16.41 
TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1L7 TCGA-E9-A1N6 
       13.48        18.51        12.92        14.07        27.42        13.48 
TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A54Y 
        6.58        22.75        23.51         0.69         1.94        23.84 
TCGA-E9-A5UP TCGA-EW-A1PC TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LL-A5YP 
       14.40         6.15       109.87        85.15        69.30        14.79 
TCGA-LL-A7T0 TCGA-OL-A5RY TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       12.36        24.72        13.12        16.80        15.39 

$`7P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       104.81        18.02        78.41       121.94        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        75.55 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       33.76        61.58       101.72       134.40        80.28       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE 
        7.30        21.30        23.21        26.96        21.14        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        17.98        53.06        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       53.98        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       18.05        15.06        36.95        13.02         0.99        28.96 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00        37.05        31.00        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
      112.08        43.00        40.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        14.01        12.00        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
        0.99        17.03        38.04         0.95        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        26.04        50.70         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        6.51         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.30         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        64.04        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       26.93       130.09         5.65        15.62        32.52        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       111.32        73.64         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       42.35        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK 
      101.95        83.87       114.02        75.55        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       48.82        76.11        43.73        43.56        39.98        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        76.21        61.28        63.62        62.14        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       85.35        50.96        83.77        79.00        89.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        93.83       143.21        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      146.50       112.37        18.77       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      140.88       211.56       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        23.05         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
        6.44        20.12       109.28         8.94        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       11.93        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        2.24         1.87         1.12         1.05         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         9.50        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.23        13.02        12.49        13.41        19.46        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        16.50        18.71        15.78        18.15 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 
       20.09        20.38        21.01        12.20        13.32        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       16.73        25.74        23.90        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        21.83        19.92        17.69        15.55        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31         6.35        12.99        15.16        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        28.60        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.99        60.53        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        20.98        11.08        54.18        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        26.56        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        35.24        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        32.09        40.24         1.12        34.65 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        41.03        12.89        20.71        17.06 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       27.22         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       26.07        18.41        30.18        15.72        12.33        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        13.81        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        17.49        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.43        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       25.05        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        14.70 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.73        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA11 
        0.16         0.26         9.93        16.50        16.93        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.16              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           176.98            234.28 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            21.90             24.79 
[1] "0.2 - 177.0 (21.9)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         7        8        1        0        43        24
  7P LOSS WILD-TYPE      82       73        7        3       310       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           1         15          5          4        0
  7P LOSS WILD-TYPE         1        135         24         59       20
                   vv
clus                STAGE TIS STAGE X
  7P LOSS MUTATED           0       0
  7P LOSS WILD-TYPE         1      13
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                 8                73
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               43               310
  STAGE IIB               24               221
  STAGE III                1                 1
  STAGE IIIA              15               135
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 0                20
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of 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 LOSS MUTATED    22  71  11   5
  7P LOSS WILD-TYPE 250 545 119  35
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              22               250
  T2              71               545
  T3              11               119
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED    58  28  17   5
  7P LOSS WILD-TYPE 443 322 100  70
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              58               443
  N1              28               322
  N2              17               100
  N3               5                70
[1] 4 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
  7P LOSS MUTATED   100   0
  7P LOSS WILD-TYPE 779  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    100    0
  7P LOSS WILD-TYPE  779   21
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0             100               779
  1               0                21
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   109   0
  7P LOSS WILD-TYPE 942  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    109    0
  7P LOSS WILD-TYPE  942   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE             109               942
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P LOSS MUTATED                            0                            93
  7P LOSS WILD-TYPE                          1                           670
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P LOSS MUTATED                                5                   2
  7P LOSS WILD-TYPE                            187                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P LOSS MUTATED                       0                                3
  7P LOSS WILD-TYPE                     4                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7P LOSS MUTATED                    0              6
  7P LOSS WILD-TYPE                 17             42
D54V8, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 93               670
  INFILTRATING LOBULAR CARCINOMA                 5               187
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 6                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    33  76
  7P LOSS WILD-TYPE 255 698
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     33   76
  7P LOSS WILD-TYPE  255  698
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               33               255
  YES              76               698
[1] 2 2
[1] FALSE
D54V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     6
  7P LOSS WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                          22    65
  7P LOSS WILD-TYPE                       148   671
D54V11, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     22               148
  WHITE                                         65               671
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  87
  7P LOSS WILD-TYPE  37 771
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   87
  7P LOSS WILD-TYPE   37  771
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              87               771
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED   100  16
  7Q LOSS WILD-TYPE 816 112
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              116               928 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               16               112 
$`7Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SO TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
        9.96        28.01        75.25        25.22        79.76        35.05 
TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A4RX 
       50.43        49.84        23.77        17.36        19.20        24.39 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A26I TCGA-A7-A6VX TCGA-A8-A06O 
       38.30        30.61        29.79        21.73        10.42        13.02 
TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I 
       29.03        17.03        53.98         9.01        18.97        14.01 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09I 
        8.98        38.01        33.01        30.97         9.99        45.07 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH 
        0.99        12.00        19.04        27.02         2.37        33.04 
TCGA-AC-A62V TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
       11.44         0.62         1.78         9.96         0.16         0.33 
TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 
        7.04         0.33         0.33         0.33        80.28        20.32 
TCGA-AO-A0JE TCGA-AO-A1KS TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A24H TCGA-AR-A24W 
       76.77         0.53        83.87        85.97       160.90        50.96 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0IC TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0WY 
       58.92        54.21        50.70       110.14       100.70       113.79 
TCGA-B6-A408 TCGA-BH-A0AZ TCGA-BH-A0BG TCGA-BH-A0DZ TCGA-BH-A0HI TCGA-BH-A0W7 
       68.12        28.50        24.85        16.27        20.38        44.81 
TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EV TCGA-BH-A1FN 
        8.81        26.66        55.63        51.39        12.00        72.07 
TCGA-BH-A42T TCGA-BH-A5J0 TCGA-C8-A12W TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM 
       10.52        23.51        12.66         4.08        10.92         2.30 
TCGA-D8-A1JE TCGA-D8-A1JJ TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.90        20.09        14.70        18.58        27.58        18.15 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H 
       14.50        16.41        12.99        13.48        18.51        12.92 
TCGA-E2-A15M TCGA-E2-A1BC TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LB TCGA-E9-A1N6 
       11.05        16.47        27.42        39.62        40.47        13.48 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A244 
        2.56         6.12        21.21         6.58        22.75         0.69 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1PC 
        1.94        24.56        26.07        23.84        14.40         6.15 
TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A5RY TCGA-S3-A6ZG 
      109.87        85.15        14.79        14.70        24.72        13.12 
TCGA-S3-AA0Z TCGA-S3-AA10 
       16.80        15.39 

$`7Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55         5.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       67.33        34.55        33.76        61.58       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV 
       80.28       107.61        74.40        72.00        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 
       44.88        44.28        17.52        17.13         8.38        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       50.47        21.90        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        31.73        23.47        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        38.37         7.30        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       29.56        31.36        24.26        23.74        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        9.37         8.75        13.02         1.02        17.98        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01         1.02        43.00        19.99        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        45.07        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
       40.01        33.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        50.04        49.05        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
        1.02        25.02         8.98        19.04        15.02        14.01 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        17.03        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       55.43        36.99        38.79        26.04        50.70         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
       16.57        19.79        23.24        24.79         1.55        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.23         0.33         2.96         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        6.51         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.59         7.17         6.28         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.33         5.59        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       32.78        21.40        52.18        26.04        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       111.32        73.64         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       42.35        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      101.95       114.02        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       85.35        83.77        79.00        89.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       72.76        93.83       143.21        20.25        62.86        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       220.90       129.57        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       74.99       103.63        71.15        24.53        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       23.93        24.95        42.35        23.05         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       20.12        90.84        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.16        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28         8.94        18.64         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
        0.39         3.16         2.24         1.87         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11        12.33        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        0.99         0.03         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        18.71        15.78        18.15        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        13.32        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69        15.55        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18         8.02        12.10        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       25.41        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        17.42        19.40         9.04        20.58 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        53.03        33.01        32.35        28.50        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        26.56        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        35.24        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
       28.27        34.95         3.02         2.76        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        34.65        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       34.13        32.05        12.53        13.32        39.09        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 
       12.89        23.51        20.71        17.06        27.22         7.13 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72        29.72         0.76        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        14.70         0.79        13.81        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        72.10        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        36.36        28.87        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.50        16.93        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.16              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           160.90            234.28 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           19.120            25.035 
[1] "0.2 - 160.9 (19.1)" "0.0 - 234.3 (25.0)"
[1] "hr=" "1.7"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         7       11        1        0        42        25
  7Q LOSS WILD-TYPE      82       70        7        3       311       220
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           1         20          4          4        1
  7Q LOSS WILD-TYPE         1        130         25         59       19
                   vv
clus                STAGE TIS STAGE X
  7Q LOSS MUTATED           0       2
  7Q LOSS WILD-TYPE         1      11
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                11                70
  STAGE IB                 1                 7
  STAGE II                 0                 3
  STAGE IIA               42               311
  STAGE IIB               25               220
  STAGE III                1                 1
  STAGE IIIA              20               130
  STAGE IIIB               4                25
  STAGE IIIC               4                59
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    25  77  12   4
  7Q LOSS WILD-TYPE 247 539 118  36
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              25               247
  T2              77               539
  T3              12               118
  T4               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED    57  34  18   7
  7Q LOSS WILD-TYPE 444 316  99  68
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              57               444
  N1              34               316
  N2              18                99
  N3               7                68
[1] 4 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
  7Q LOSS MUTATED   105   1
  7Q LOSS WILD-TYPE 774  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    105    1
  7Q LOSS WILD-TYPE  774   20
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0             105               774
  1               1                20
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED   117   1
  7Q LOSS WILD-TYPE 934  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    117    1
  7Q LOSS WILD-TYPE  934   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE             117               934
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q LOSS MUTATED                            0                            98
  7Q LOSS WILD-TYPE                          1                           665
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q LOSS MUTATED                               11                   0
  7Q LOSS WILD-TYPE                            181                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q LOSS MUTATED                       0                                3
  7Q LOSS WILD-TYPE                     4                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7Q LOSS MUTATED                    0              6
  7Q LOSS WILD-TYPE                 17             42
D55V8, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 98               665
  INFILTRATING LOBULAR CARCINOMA                11               181
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 6                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    37  81
  7Q LOSS WILD-TYPE 251 693
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     37   81
  7Q LOSS WILD-TYPE  251  693
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               37               251
  YES              81               693
[1] 2 2
[1] FALSE
D55V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     6
  7Q LOSS WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                          20    73
  7Q LOSS WILD-TYPE                       150   663
D55V11, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     20               150
  WHITE                                         73               663
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  94
  7Q LOSS WILD-TYPE  38 764
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   94
  7Q LOSS WILD-TYPE   38  764
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              94               764
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   329  59
  8P LOSS WILD-TYPE 587  69
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              388               656 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               59                69 
$`8P LOSS MUTATED`
TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       42.81        11.44        31.79        39.32        28.01        19.20 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y 
       18.02        78.41        73.84        87.25        63.12        36.13 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 
       99.12       114.81        92.48         5.19       107.93        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SX 
       25.22        34.29        31.82        61.94        24.72        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YT 
       17.52        17.13        49.84        21.67        19.33        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A3XT 
       17.36        60.72        19.56        42.44        18.15        83.01 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A13D 
       29.98        50.37         7.30        21.90        37.45        31.73 
TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SE 
       20.19        23.74        20.61        10.59        11.28        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       17.92        14.73        12.10        13.02        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       53.06        17.03        19.99        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08J 
        7.99         9.99        15.06        36.95        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09D 
       31.00        33.01        43.00        33.01        12.00        50.04 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A7 
       29.98         1.02        25.02         8.98        19.04         0.99 
TCGA-AC-A23H TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A7VB 
        5.72        50.70        33.04        14.99        16.57         8.22 
TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
       20.19         0.33         0.23         0.62         2.96         1.78 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FS TCGA-AN-A0FV 
        0.16         0.33         0.33         6.44         6.28         0.33 
TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J2 
        0.33        66.77        81.63        95.70        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        52.18        26.04        37.48        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       50.70        76.77        26.24        55.33        71.80       102.58 
TCGA-AO-A126 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04L 
      108.72        64.04        41.62        70.39        17.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        5.65        15.62       111.32        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       98.93        64.83        55.86       101.95        83.87       114.02 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       52.77        51.25        76.11        39.98        17.23        37.81 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24U 
       63.62        62.14       160.90        50.89        94.22        53.36 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LE TCGA-AR-A5QQ TCGA-B6-A0I1 
       85.35        79.00        89.00       143.21        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
      143.38        12.13       146.50       176.98        18.77       126.12 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT 
      140.88        68.45       100.70       131.21        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A408 
       18.35       113.79        68.94        58.88       139.17        68.12 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0B7 
       71.15        59.84        25.55        40.83        56.94        56.98 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 
       44.05        48.69        53.69        49.94        41.75        42.90 
TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       23.44        48.23         9.63        24.49        31.00        24.43 
TCGA-BH-A0H7 TCGA-BH-A0HK TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       23.08         5.85        51.32        27.25        50.79        23.93 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       42.35        23.05         8.81         7.23        20.12        90.84 
TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.74        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD 
       55.69        17.69        25.81        31.53        24.66        33.17 
TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 
       36.92        72.07        72.07        28.14        38.60        57.83 
TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
      130.16         8.94        18.87         9.44        11.77        11.77 
TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       11.77         0.39         2.24         1.87         1.12         4.11 
TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
        4.08        11.34        11.28        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
        3.25         0.23         9.50        12.20         0.99         0.23 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        11.90        20.88        13.25 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        13.48        14.17        17.49        15.78        18.15 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JT TCGA-D8-A1X8 TCGA-D8-A1XD 
       12.03        20.09        20.12        13.32        25.74        17.16 
TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       21.83        17.69        16.41        16.31        15.52        14.24 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
       16.04        13.05        16.41        13.48        10.09        12.26 
TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C 
       18.51        16.18        43.00        27.52        40.41        40.11 
TCGA-E2-A14N TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       47.15        33.17        33.30        34.26        32.02        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15J 
       18.51        25.41        23.34        22.82        12.92        19.40 
TCGA-E2-A15K TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF 
        9.04        17.06        53.62        32.35        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 
       32.78        33.73        33.70        20.98        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       39.62        28.90        18.87       102.61         8.75        43.04 
TCGA-E2-A56Z TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
        8.28        26.56        12.85        12.00        13.12        12.59 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF 
       35.24         9.86         3.02        21.21        34.65         6.58 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       34.59        34.13        13.32        39.09        41.03        12.89 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1IX TCGA-EW-A1OV 
        0.69         1.94        30.18        23.84        39.72        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PA 
       22.82        29.85        40.41        52.96         7.86        18.90 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       10.52        14.43        19.96        55.00        52.73        25.91 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A3NW 
       17.49        23.51       109.87        59.57       216.76       110.50 
TCGA-GM-A3XL TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 
       69.30        13.55        62.43        11.84        11.57         7.10 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        24.95        11.44        25.05        15.32        14.70 
TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW TCGA-OL-A5RY 
       16.08        12.36        14.73        14.07        36.36        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66P TCGA-PE-A5DC TCGA-PE-A5DD 
       22.32        20.38        65.62        14.07        47.01        64.21 
TCGA-PE-A5DE TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       86.96        16.93        14.96        13.94        17.03         3.81 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

$`8P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R 
       20.88        13.68         7.96        18.21       104.81       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CQ TCGA-A2-A0CR 
      101.98        55.43       136.73        24.79        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       75.55        75.25        98.99        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       74.40        72.00        35.05        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       27.12        44.88        44.28         8.38        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       21.90        49.48        18.61        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.20        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       17.19       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       32.75        49.48        47.31        34.98        38.37        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        30.61        35.67        33.11        29.79 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       25.15        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       21.73        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        13.74        14.50        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06U 
       10.29         9.37        10.42         8.75         1.02        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07R TCGA-A8-A07U 
       18.97        18.97        14.01        12.00         8.98        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       45.07        18.05        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       33.01        12.00         9.99        31.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       40.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09V 
       12.00         1.02        49.05        45.07        33.07        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        26.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83        22.19        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         0.03         1.12         1.32         2.30         0.33 
TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.33         1.71         9.96         7.36         6.51         0.33 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT 
        5.65         7.96         7.00         7.59         7.17         7.04 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV 
        0.36         0.33         0.33         0.30         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        80.28        61.35        68.75        47.87        58.95 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI 
       20.32        22.36        50.86        72.00        21.37        50.24 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       62.04        99.25       106.78       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        48.36        28.37        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
        0.53        24.79        26.93        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U4 
       19.20        73.64         5.26       107.24        65.36        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       75.55        61.84        48.82        43.73        43.56        43.07 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       76.21        61.28        33.73        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W 
        2.76       104.28        87.22        97.84        76.01        50.96 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       83.77        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH 
      149.59       220.90       129.57        50.70        65.72       112.37 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93       211.56       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       89.46       157.41        79.63        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
      186.48        28.27        43.59       101.52        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ 
       85.35        74.99       103.63        24.53        20.45        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA 
       46.95        39.55        39.16        48.36        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       35.67        27.19        53.95        45.57        11.67        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       44.02        48.13        45.83        31.17        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        46.19        32.58        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX 
       20.38         2.50        13.61        36.85        12.89         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P 
       24.95        44.81         2.01        26.66        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       55.63        37.55        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       12.00        49.58        89.16        97.48       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
       74.73       122.89        63.35        55.00        45.63       144.59 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       26.14        83.31        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8G0 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       21.76        11.93        12.66        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.66        12.66         3.16         1.05        12.33        10.92 
TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.16         0.30         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A142 
        9.53         0.03         0.03        13.02        20.58        13.97 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF 
       21.14        19.20        16.50        18.71        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X9 
       12.20        14.70        18.58        17.79        16.73        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15        12.39        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       19.92        15.55        15.85         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       12.66        16.54        15.32         9.93        14.14        17.42 
TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       13.45        14.43         9.44         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 
       12.53        33.37        21.67         8.02        12.10        34.42 
TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       46.59        37.51        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       38.24        38.60        43.33        28.60        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D 
       19.43        21.04        23.87        14.79        25.05        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15L TCGA-E2-A15M 
       20.71        21.63        18.21        17.42        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       13.02        19.56        14.07        14.99        60.53        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IJ TCGA-E2-A1IK 
       33.01        28.50        16.47        17.10        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        22.19        11.08        19.66        24.59        40.47 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      106.75        16.93         5.52        15.72        30.61        34.92 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA 
       34.29        34.82        32.88        36.82        13.48        36.56 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       39.55        35.77        25.84        11.90        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        2.56         6.12         2.76        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B 
        1.12        21.27        35.64        32.05        12.53        22.75 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       23.51        20.71        17.06        27.22         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.72        29.72         0.76        26.07        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       15.68        28.77        29.95        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       23.11        18.48        30.08        19.99         6.15        13.94 
TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB 
       34.55        22.09        34.03        10.16         7.40        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62        85.35        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A74U 
       66.38        72.03        18.12         2.60        21.24        13.22 
TCGA-LD-A9QF TCGA-LL-A442 TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       10.62        10.95        17.06        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 
        2.63        15.68         7.46        14.50        14.70        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K 
       40.08        34.92        28.87        26.70        23.47        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        17.36        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
        8.91         0.16         0.26         9.93        16.50        13.12 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-W8-A86G 
       16.80        15.39        13.84        15.35        13.84        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 
       52.96       108.07 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.16              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           216.76            234.28 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            24.69             24.46 
[1] "0.2 - 216.8 (24.7)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.5"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED        32       30        3        0       134        89
  8P LOSS WILD-TYPE      57       51        5        3       219       156
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         59          9         24        7
  8P LOSS WILD-TYPE         2         91         20         39       13
                   vv
clus                STAGE TIS STAGE X
  8P LOSS MUTATED           0       5
  8P LOSS WILD-TYPE         1       8
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 32                57
  STAGE IA                30                51
  STAGE IB                 3                 5
  STAGE II                 0                 3
  STAGE IIA              134               219
  STAGE IIB               89               156
  STAGE III                0                 2
  STAGE IIIA              59                91
  STAGE IIIB               9                20
  STAGE IIIC              24                39
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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   101 237  39  16
  8P LOSS WILD-TYPE 171 379  91  24
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1             101               171
  T2             237               379
  T3              39                91
  T4              16                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED   184 125  50  27
  8P LOSS WILD-TYPE 317 225  67  48
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             184               317
  N1             125               225
  N2              50                67
  N3              27                48
[1] 4 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
  8P LOSS MUTATED   334   7
  8P LOSS WILD-TYPE 545  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    334    7
  8P LOSS WILD-TYPE  545   14
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             334               545
  1               7                14
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   390   3
  8P LOSS WILD-TYPE 661   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    390    3
  8P LOSS WILD-TYPE  661    8
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             390               661
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P LOSS MUTATED                            1                           311
  8P LOSS WILD-TYPE                          0                           452
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P LOSS MUTATED                               50                   2
  8P LOSS WILD-TYPE                            142                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P LOSS MUTATED                       0                                7
  8P LOSS WILD-TYPE                     4                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8P LOSS MUTATED                    3             18
  8P LOSS WILD-TYPE                 14             30
D56V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                311               452
  INFILTRATING LOBULAR CARCINOMA                50               142
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                18                30
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   111 282
  8P LOSS WILD-TYPE 177 492
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    111  282
  8P LOSS WILD-TYPE  177  492
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              111               177
  YES             282               492
[1] 2 2
[1] FALSE
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1    31
  8P LOSS WILD-TYPE                                0    29
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          67   260
  8P LOSS WILD-TYPE                       103   476
D56V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         31                29
  BLACK OR AFRICAN AMERICAN                     67               103
  WHITE                                        260               476
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11 326
  8P LOSS WILD-TYPE  27 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  326
  8P LOSS WILD-TYPE   27  532
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                27
  NOT HISPANIC OR LATINO             326               532
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    76  14
  8Q LOSS WILD-TYPE 840 114
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               90               954 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               114 
$`8Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SO TCGA-A2-A0CU TCGA-A2-A3XZ TCGA-A7-A0D9 TCGA-A7-A13E 
       42.81        28.01         5.19        50.37        37.45        20.19 
TCGA-A7-A4SF TCGA-A8-A07L TCGA-A8-A097 TCGA-A8-A09D TCGA-AC-A2FO TCGA-AC-A3W5 
       17.92        32.05        12.00        50.04        50.70        16.57 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0XO TCGA-AO-A03P TCGA-AO-A0J2 
        0.23         2.96         6.44        12.33        95.70        32.78 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AQ-A0Y5 
       53.03        21.53        55.33        71.80       102.58         5.65 
TCGA-AR-A0TY TCGA-AR-A0U3 TCGA-AR-A24H TCGA-AR-A24K TCGA-B6-A0IK TCGA-B6-A0IQ 
       55.86       114.02       160.90        50.89        18.77       140.88 
TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0X5 TCGA-B6-A408 TCGA-BH-A0B7 
       68.45       100.70        97.48        68.94        68.12        56.98 
TCGA-BH-A0BR TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0W3 
       53.69        42.90        23.44        24.49        31.00        23.93 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-C8-A12P 
       66.05         7.36        69.93        24.66        33.17        11.77 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HL 
        1.87         1.12         4.11         4.08        11.28        10.42 
TCGA-C8-A26W TCGA-C8-A8HQ TCGA-D8-A140 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 
        0.23        12.49        13.25        13.48        14.17        17.49 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A14V TCGA-E2-A15K TCGA-E2-A1IG 
       12.26        18.51        16.18        34.26         9.04        32.78 
TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E9-A1N8 TCGA-E9-A1R5 
       33.73        39.62        18.87        43.04        12.00         3.02 
TCGA-E9-A1R7 TCGA-E9-A22D TCGA-E9-A244 TCGA-EW-A1PE TCGA-EW-A3U0 TCGA-EW-A424 
       21.21        41.03         0.69        10.52        17.49        23.51 
TCGA-LL-A440 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66P 
       24.95        14.73        36.36        22.32        20.38        14.07 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-WT-AB44 TCGA-XX-A899 
       64.21        86.96        16.93        14.96        29.03        15.35 

$`8Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55        75.25        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        32.75        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       47.31        34.98        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        30.61        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       38.01        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
        9.99        31.00        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       43.00        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
        9.99         9.99        12.00         1.02        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         5.72         1.48        38.53        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        26.04        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       14.99        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.28         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       50.24        62.04        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93       130.09        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ 
       74.79        86.66        42.35        98.93        64.83       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14        33.73        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        54.21        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH 
      126.12        84.59       110.14       110.93       211.56       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48        89.46       131.21       157.41       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       18.35        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        74.99       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        48.36        56.94        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        35.67        48.69        27.19        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        46.19        32.58        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        7.23        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       30.28        55.63        37.55        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28         8.94        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        1.05        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        2.30         3.25         0.30         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.03         0.23        13.02        13.41        19.46        11.90 
TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 
       20.88        20.58        13.97        14.17        21.14        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        15.55        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31         6.35        12.99        15.16        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       33.37        21.67         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        33.30        43.33        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       18.51        25.41        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II 
       28.50        16.47        17.10        38.30        37.41        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        19.66        24.59        40.47        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        13.48        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       39.55        12.59        35.77        35.24        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 
       11.90        28.27        34.95         2.56         6.12         2.76 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        32.09        40.24         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       12.33        23.84        14.70         0.79        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        13.94        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       55.00        52.73        25.91        22.09        34.03        10.16 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        11.44        10.95        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        14.70        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       14.07        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        28.21        19.73        40.11         8.91        47.01 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z 
        0.16         0.26         9.93        16.50        13.12        16.80 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       15.39        13.84        15.35        13.84        13.94        17.03 
TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.81        11.41        52.96        16.04       108.07       107.05 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           160.90            234.28 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           23.475            24.655 
[1] "0.2 - 160.9 (23.5)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.5"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         6        7        0        0        30        26
  8Q LOSS WILD-TYPE      83       74        8        3       323       219
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0         13          3          5        0
  8Q LOSS WILD-TYPE         2        137         26         58       20
                   vv
clus                STAGE TIS STAGE X
  8Q LOSS MUTATED           0       1
  8Q LOSS WILD-TYPE         1      12
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  6                83
  STAGE IA                 7                74
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               30               323
  STAGE IIB               26               219
  STAGE III                0                 2
  STAGE IIIA              13               137
  STAGE IIIB               3                26
  STAGE IIIC               5                58
  STAGE IV                 0                20
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of 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    19  59  10   3
  8Q LOSS WILD-TYPE 253 557 120  37
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              19               253
  T2              59               557
  T3              10               120
  T4               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED    39  36   9   5
  8Q LOSS WILD-TYPE 462 314 108  70
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              39               462
  N1              36               314
  N2               9               108
  N3               5                70
[1] 4 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
  8Q LOSS MUTATED    74   0
  8Q LOSS WILD-TYPE 805  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     74    0
  8Q LOSS WILD-TYPE  805   21
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              74               805
  1               0                21
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    91   0
  8Q LOSS WILD-TYPE 960  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     91    0
  8Q LOSS WILD-TYPE  960   11
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              91               960
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q LOSS MUTATED                            0                            70
  8Q LOSS WILD-TYPE                          1                           693
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q LOSS MUTATED                               15                   0
  8Q LOSS WILD-TYPE                            177                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q LOSS MUTATED                       0                                1
  8Q LOSS WILD-TYPE                     4                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8Q LOSS MUTATED                    3              2
  8Q LOSS WILD-TYPE                 14             46
D57V8, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 70               693
  INFILTRATING LOBULAR CARCINOMA                15               177
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 2                46
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19  72
  8Q LOSS WILD-TYPE 269 702
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19   72
  8Q LOSS WILD-TYPE  269  702
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               19               269
  YES              72               702
[1] 2 2
[1] FALSE
D57V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0    10
  8Q LOSS WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                          21    56
  8Q LOSS WILD-TYPE                       149   680
D57V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     21               149
  WHITE                                         56               680
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4  77
  8Q LOSS WILD-TYPE  34 781
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4   77
  8Q LOSS WILD-TYPE   34  781
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO              77               781
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   258  44
  9P LOSS WILD-TYPE 658  84
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              302               742 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               44                84 
$`9P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL 
      129.14       131.67        13.68        28.01        18.02        99.12 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       75.25        67.33        80.28        79.76        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH 
       27.12        44.88        17.52        18.21        21.90        21.67 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E 
       23.77        17.36        60.72        19.20        42.44       105.34 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CJ 
       33.93        32.75        47.31        34.98        26.96        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G 
       37.45        35.67        29.79        31.73        25.15        23.74 
TCGA-A7-A2KD TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O 
       22.32        14.93        13.74        17.92        10.29        13.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        29.03         1.02        17.03         9.01        43.00 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       18.97         9.99        19.96        12.00        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       31.00         0.99        12.00         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        33.07         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       19.04         0.99        19.04        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       17.03        99.35        55.43        33.04         0.92         2.27 
TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
       11.44        13.58         0.03        20.19         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.23         0.62         2.96         1.78         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS 
        6.51         0.16         7.96         0.36         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V 
        0.33         5.59        80.28        66.77        81.63        29.13 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A12F 
       52.18        26.04        21.53        72.00        76.77        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       61.87         0.53        17.79       130.09         5.65        15.62 
TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TY 
       32.91        73.64         5.26        74.79        42.35        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24N 
       61.84        39.98        43.07        63.62        50.89        78.51 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 
       87.22        97.84        85.35        50.96        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 TCGA-B6-A0IB 
       73.18        58.92        54.21        66.15        12.13       129.57 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW 
       18.77       110.14       162.05       102.77        79.63        18.35 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 
       85.35        68.12        24.53        20.45        28.50        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       48.36        56.98        25.71        44.05        48.69        53.69 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DK 
       49.94        11.67        48.13        42.90        22.13        13.91 
TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 
        3.22         9.63        24.49        30.35        10.78        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18K TCGA-BH-A18L 
       41.00        52.96        50.79        23.93        90.84        26.66 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F2 
        7.36        51.39        69.93       113.82        17.69        31.53 
TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 
       24.66        45.63        72.07        72.07        57.83       130.16 
TCGA-BH-A42T TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
       10.52         9.44        11.93        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG 
       12.66        12.66         3.16         2.24         4.11        11.34 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27B 
       10.42         2.30         0.30         0.43         9.67         0.99 
TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JC 
       13.41        11.90        20.88        14.17        13.48        15.78 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1X6 
       12.03        20.09        20.12        19.40        18.58        17.79 
TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY 
       27.58        17.16        16.41        16.31         6.35        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 
       14.14        16.04         4.80        10.09        12.26        46.59 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z 
       44.68        38.60        33.30        32.02        31.96        18.51 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15S 
       27.12        23.34        20.71        21.63        12.92        14.07 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 
       24.59        40.47       106.75       102.61         8.75        34.92 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 
       13.12        36.56        35.24         9.86        11.90        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE 
        6.12         2.76        21.21        32.09        40.24        34.65 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A5UO 
       21.27        34.59        39.09        22.75        12.89        13.81 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 
       14.40        28.77        25.94        22.82        29.85        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FR TCGA-EW-A2FS 
       29.82        23.11        18.90        13.94        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2DB 
       25.91        34.03        10.16        23.51       109.87        79.10 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FQ 
        2.60        11.57         7.10        11.44        14.79         2.63 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D6 TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A66P 
       14.70        12.36        36.30        22.32        26.04        14.07 
TCGA-PE-A5DC TCGA-S3-A6ZH 
       47.01        16.93 

$`9P LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO 
      101.98        55.43        36.13       136.73        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        75.55         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV 
      101.72       134.40       107.61        74.40        72.00        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX 
       61.94        24.72        63.29        99.19        54.64        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI 
       18.90        20.75        32.55        25.28        50.47        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       18.61        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       18.15        10.59        20.88        39.65        83.01        29.98 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        50.37        38.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.47        33.11        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD 
       10.29        11.28        13.41        14.70        11.97        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       21.17        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
       10.42         8.75        13.02         1.02        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       26.01        53.98        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S TCGA-A8-A08T 
       38.01        28.96        33.01         9.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       43.00        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 
        9.99        50.04        29.98        15.02        14.01        12.00 
TCGA-A8-A0A4 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       13.02        38.04         0.95         2.37        10.85         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
        1.48        38.53        40.57        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
       50.70        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
       16.57        19.79        23.24        24.79         1.55        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OQ 
       17.42        18.67        12.26         1.68         8.22         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0AS 
        1.32         2.30         0.33         1.71         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        6.28         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV 
        0.33        12.33         0.30         0.33         0.33         5.33 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 
       61.35        95.70        68.75        47.87        58.95        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB 
       21.40        37.48        20.32        22.36        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        64.04        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 
       14.73        82.62        70.39        24.79        26.93        32.52 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
        2.56        19.20       111.32        86.66        98.93        64.83 
TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       65.36        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX 
       43.56        17.23        37.81        76.21        61.28        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P 
       33.73       160.90        94.22        96.89        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 
      104.28        76.01        53.36        83.77        89.00        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       143.21        20.25        62.86        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       143.38       149.59       220.90        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       176.98       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       81.17        78.02       172.96       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WY 
      131.21       157.41        97.48       188.68        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 
       43.59       101.52        73.51       139.17       170.17        74.99 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
      103.63        71.15        59.84        25.55        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        56.94        51.68        37.22        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       24.85        21.70        61.68        35.67        27.19        53.95 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE 
       45.57        49.05        41.75        44.02        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       23.44        38.01        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30        44.81        46.19        32.58        31.00        24.43 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI 
       15.16        37.78        35.51        24.56        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
        8.81         2.01         7.23        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EO 
       30.28        55.63        37.55        66.05        51.16        91.99 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       82.85        42.28        12.00        55.69        49.58        25.81 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A201 
      122.89        36.92        63.35        55.00       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       26.14        38.60        83.31        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q 
        9.70        18.87        21.76        11.77        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 
       12.66         0.39         1.87         1.12         1.05         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN 
       12.33        10.92        11.28         0.16        12.03         3.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.23         0.36         8.28         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ 
       12.20         0.03         0.23        13.02        12.49        19.46 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        13.97        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        18.71        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       13.32        14.70        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       17.69        15.55        15.85        12.99        15.16        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       15.32        15.52         9.93        14.24        17.42        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P 
       13.05        14.43         9.44        16.41        13.48         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.53        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
        8.02        12.10        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A150 
       38.24        33.17        43.33        34.26        28.60        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       22.82        17.29        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
       20.58        11.05        13.02        19.56        17.06        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LE 
       11.08        54.18        27.42        39.62        19.66        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       18.87        43.04        16.93         5.52        15.72         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        26.56        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       36.82        13.48        12.00        39.55        12.59        35.77 
TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RD 
       25.84        28.27         2.56         3.02        32.09         1.12 
TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.03        23.51        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41        30.18        15.72        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70         0.79        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX 
       18.21        18.90        13.25        16.57        15.68        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       40.41        41.13        39.78        18.48        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        10.52        14.43        34.55        19.96 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       22.09        17.49         7.40        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
       22.26        16.08        15.68         7.46        14.50        14.73 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.07        27.91        22.39         2.10        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD 
       17.36        28.21        19.73        40.11         8.91        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        16.50        13.12 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           162.05            234.28 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           23.625            24.790 
[1] "0.0 - 162.1 (23.6)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.6"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED        21       15        0        0       104        61
  9P LOSS WILD-TYPE      68       66        8        3       249       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         53         16         19       10
  9P LOSS WILD-TYPE         1         97         13         44       10
                   vv
clus                STAGE TIS STAGE X
  9P LOSS MUTATED           0       5
  9P LOSS WILD-TYPE         1       8
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 21                68
  STAGE IA                15                66
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA              104               249
  STAGE IIB               61               184
  STAGE III                1                 1
  STAGE IIIA              53                97
  STAGE IIIB              16                13
  STAGE IIIC              19                44
  STAGE IV                10                10
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    55 198  34  18
  9P LOSS WILD-TYPE 217 418  96  22
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              55               217
  T2             198               418
  T3              34                96
  T4              18                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED   139  89  49  24
  9P LOSS WILD-TYPE 362 261  68  51
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             139               362
  N1              89               261
  N2              49                68
  N3              24                51
[1] 4 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
  9P LOSS MUTATED   255  11
  9P LOSS WILD-TYPE 624  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    255   11
  9P LOSS WILD-TYPE  624   10
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             255               624
  1              11                10
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   300   6
  9P LOSS WILD-TYPE 751   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    300    6
  9P LOSS WILD-TYPE  751    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             300               751
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P LOSS MUTATED                            0                           256
  9P LOSS WILD-TYPE                          1                           507
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P LOSS MUTATED                               24                   3
  9P LOSS WILD-TYPE                            168                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P LOSS MUTATED                       1                                9
  9P LOSS WILD-TYPE                     3                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9P LOSS MUTATED                    3             10
  9P LOSS WILD-TYPE                 14             38
D58V8, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                256               507
  INFILTRATING LOBULAR CARCINOMA                24               168
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                10                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    96 210
  9P LOSS WILD-TYPE 192 564
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     96  210
  9P LOSS WILD-TYPE  192  564
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               96               192
  YES             210               564
[1] 2 2
[1] FALSE
D58V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0    21
  9P LOSS WILD-TYPE                                1    39
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          50   196
  9P LOSS WILD-TYPE                       120   540
D58V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         21                39
  BLACK OR AFRICAN AMERICAN                     50               120
  WHITE                                        196               540
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    12 239
  9P LOSS WILD-TYPE  26 619
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12  239
  9P LOSS WILD-TYPE   26  619
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                26
  NOT HISPANIC OR LATINO             239               619
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   239  36
  9Q LOSS WILD-TYPE 677  92
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              275               769 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               36                92 
$`9Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
      129.14        13.68         7.96        28.01        18.02       101.98 
TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET 
       99.12        75.25        67.33        80.28        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       34.29        50.43        18.21        21.90        21.67        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX 
       17.36        60.72        19.20        33.93        32.75        47.31 
TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA 
       34.98        26.96        21.90        35.31        37.45        35.67 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SB 
       29.79        31.73        25.15        23.74        22.32        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       14.50        17.92        10.29        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G 
       53.06        31.00         1.02         9.01        43.00        18.97 
TCGA-A8-A07R TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
        8.98        33.01        12.00        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I 
        0.99        43.00        12.00        12.00         1.02        45.07 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 
       33.07        25.02        19.04        19.04        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI 
       27.02        17.03        99.35        55.43        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X 
        2.27        11.44        13.58         0.03        20.19         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FJ 
        0.33         0.23         1.78         7.36         0.16         7.96 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L 
        0.36         0.33         0.33         0.33         5.59        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       66.77        81.63        29.13        21.40        52.18        26.04 
TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       72.00        55.33        48.36        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O 
       17.79       130.09         5.65        15.62         2.56        32.91 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       73.64        74.79        55.86       107.24        65.36       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ 
      114.02        85.97        75.55        61.84        39.98        43.07 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S 
       63.62        33.73        50.89        78.51        87.22        97.84 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A2LL 
       85.35        79.00        78.48        73.18        54.21        66.15 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO 
       12.13       129.57       110.14       211.56        81.17       162.05 
TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A401 
      102.77        79.63        18.35        21.47        43.59        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       74.99        68.12        24.53        39.55        48.36        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C3 
       51.68        25.71        44.05        45.57        49.94        48.13 
TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ 
        3.22         4.41         9.63        24.49        30.35        10.78 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0W3 TCGA-BH-A18K TCGA-BH-A18Q 
       23.08        41.00        52.96        23.93        90.84        55.63 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FE 
        7.36        69.93       113.82        24.66        33.17        74.73 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42T 
       45.63        72.07        72.07        57.83       130.16        10.52 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W 
        9.44        11.93        12.66        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HJ TCGA-C8-A26X 
       12.66         3.16         2.24         4.11         0.16         0.36 
TCGA-C8-A26Z TCGA-C8-A27B TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 
        8.28         0.99        13.41        20.88        14.17        13.48 
TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1X6 
       15.78        18.97        20.09        20.12        18.58        17.79 
TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y3 
       27.58        17.16        16.41        16.31        16.54        14.14 
TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R 
       16.04        10.09        12.26        46.59        44.68        38.60 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 
       32.02        31.96        18.51        25.41        27.12        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A1AZ TCGA-E2-A1LB TCGA-E2-A1LH 
       23.34        20.71        21.63        60.53        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
      102.61         8.75        34.92        13.12        36.56        39.55 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
        9.86        11.90         6.12         2.76        21.21        40.24 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22B TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J6 
       21.27        34.59        22.75        13.81        14.40        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A2FR 
       25.94        22.82        29.85        52.96        23.11        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        25.91        34.03        17.49        10.16        23.51 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM 
      109.87        79.10         2.60        11.57        11.44        15.32 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ 
       14.79         2.63        16.08        14.70        12.36        22.32 
TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZF TCGA-S3-A6ZH 
       20.38        26.04        14.07        16.50        16.93 

$`9Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        20.88        31.79        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
      134.40       107.61        74.40        72.00        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 
       39.65        83.01        29.98        49.48        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30        24.39        21.30        23.21        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       34.29        35.47        30.61        33.11        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        24.26        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06U 
       11.05         9.37        10.42         8.75        13.02        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       26.01        17.03        53.98        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        45.07        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08S 
        0.99        38.01        28.96        19.96         9.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
      112.08        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09N 
        9.99         9.99        50.04        49.05        29.98         1.02 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        15.02         0.99        14.01        12.00        13.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       38.53        40.57        36.99        38.79        26.04        50.70 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AC-A8OR 
       18.67        12.26         1.68         8.22         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        2.30         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         7.04         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R 
        0.33         0.33         5.33        61.35        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       47.87        58.95        32.78        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04H 
       57.30        41.62        28.37        14.73        82.62        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT 
       26.93        32.52        19.20       111.32         5.26        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AJ TCGA-AR-A1AK 
       42.35        98.93        64.83        83.87        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS 
       48.82        76.11        43.73        43.56        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       76.21        61.28        62.14       160.90        94.22        96.89 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
       84.20         2.76       104.28        76.01        53.36        50.96 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       83.77        89.00        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        62.86        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      143.38       149.59       220.90        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       176.98        18.77       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88        68.45       189.01       234.28        78.02       172.96 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88       101.52        73.51       139.17       170.17 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      103.63        71.15        59.84        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC 
       46.95        40.83        39.16        56.94        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.69        53.95        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       44.02        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        67.86        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 
       44.81        46.19        32.58        31.00        24.43        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       37.78        35.51        24.56        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01         7.23        20.12        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V 
       37.74        30.28        37.55        66.05        51.39        51.16 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
      114.15       122.89        36.92        63.35        55.00       144.59 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       28.14        26.14        38.60        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12       109.28         8.94        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12N 
        5.26         9.70        18.87        21.76        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         0.39         1.87         1.12         1.05 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        4.08        12.33        10.92        11.34        11.28        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       10.42         2.30         3.25         0.30         0.23         0.43 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
        9.67         9.53         0.03         9.50        12.20         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
        0.23        13.02        12.49        19.46        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        18.71        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       13.32        14.70        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       17.69        15.55        15.85         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.66        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18         8.02        12.10        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       47.15        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        28.60        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       14.79        22.82        17.29        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       19.66        24.59        28.90        18.87        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         8.28        30.61        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       12.85        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R2 
       12.59        35.77        35.24        25.84        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE 
        2.56         3.02        32.09        32.09         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        35.64        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        41.03        12.89        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        23.84        14.70         0.79        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       15.68        29.95        40.41        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FW 
       13.94        10.52        14.43        34.55        19.96        22.09 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
        7.40        59.57       216.76        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U 
       72.03        13.55        18.12        62.43        11.84        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 
       13.22         7.10        13.28        10.62        24.95        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A73Y 
       25.05        17.06        14.70        14.47        22.26        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I 
       34.92        36.36        28.87        24.72        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ 
       65.62        41.92        42.77        17.36        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        13.12        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           211.56            234.28 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            25.02             24.39 
[1] "0.0 - 211.6 (25.0)" "0.0 - 234.3 (24.4)"
[1] "hr=" "1.2"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED        19       16        0        0        98        55
  9Q LOSS WILD-TYPE      70       65        8        3       255       190
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         45         12         19        7
  9Q LOSS WILD-TYPE         1        105         17         44       13
                   vv
clus                STAGE TIS STAGE X
  9Q LOSS MUTATED           0       5
  9Q LOSS WILD-TYPE         1       8
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 19                70
  STAGE IA                16                65
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               98               255
  STAGE IIB               55               190
  STAGE III                1                 1
  STAGE IIIA              45               105
  STAGE IIIB              12                17
  STAGE IIIC              19                44
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of 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    52 173  35  16
  9Q LOSS WILD-TYPE 220 443  95  24
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              52               220
  T2             173               443
  T3              35                95
  T4              16                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q LOSS MUTATED   133  79  39  23
  9Q LOSS WILD-TYPE 368 271  78  52
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             133               368
  N1              79               271
  N2              39                78
  N3              23                52
[1] 4 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
  9Q LOSS MUTATED   230   8
  9Q LOSS WILD-TYPE 649  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    230    8
  9Q LOSS WILD-TYPE  649   13
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             230               649
  1               8                13
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   272   6
  9Q LOSS WILD-TYPE 779   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    272    6
  9Q LOSS WILD-TYPE  779    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             272               779
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q LOSS MUTATED                            0                           230
  9Q LOSS WILD-TYPE                          1                           533
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q LOSS MUTATED                               21                   2
  9Q LOSS WILD-TYPE                            171                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q LOSS MUTATED                       1                                9
  9Q LOSS WILD-TYPE                     3                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9Q LOSS MUTATED                    3             12
  9Q LOSS WILD-TYPE                 14             36
D59V8, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                230               533
  INFILTRATING LOBULAR CARCINOMA                21               171
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                12                36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    91 187
  9Q LOSS WILD-TYPE 197 587
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     91  187
  9Q LOSS WILD-TYPE  197  587
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               91               197
  YES             187               587
[1] 2 2
[1] FALSE
D59V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0    18
  9Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          54   173
  9Q LOSS WILD-TYPE                       116   563
D59V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     54               116
  WHITE                                        173               563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    11 216
  9Q LOSS WILD-TYPE  27 642
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11  216
  9Q LOSS WILD-TYPE   27  642
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                27
  NOT HISPANIC OR LATINO             216               642
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   141  25
  10P LOSS WILD-TYPE 775 103
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               166                878 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                103 
$`10P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67         9.96        13.68        31.79        39.32 
TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       19.20        73.84        75.55        75.25         5.19       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4RW 
       67.33        25.22        18.21        17.36        60.72         7.30 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26E 
       24.39        26.96        21.90        30.61        25.15        31.36 
TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I 
       22.32        13.74        21.17        17.98        53.98        14.01 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09B 
       15.06        33.01        12.00         9.99        12.00        12.00 
TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23H TCGA-AC-A2QH 
        8.98        21.04        17.03        38.04         5.72        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VC 
        0.92         2.27        17.42        13.58        12.26         0.03 
TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XN 
        0.62         7.36         0.33         0.33         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U 
        0.30         0.33         0.33        61.35        66.77        58.95 
TCGA-AO-A0JD TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0U2 
       72.00        48.36        26.93         5.26        42.35        83.87 
TCGA-AR-A1AN TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 
       43.73        94.22       104.28        87.22        50.96        89.00 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QQ 
       72.76        93.83        54.21        39.39        20.38        10.59 
TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN 
       18.77        81.17       100.70       131.21        73.51       139.17 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ 
       68.12        24.53        39.55        56.98        37.22        21.70 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0EB 
       45.57        49.94        49.05        44.02        42.90        24.49 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18V 
       41.00        52.96        51.32        23.05         7.23        51.16 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN 
       91.99        42.28        24.66        36.92        45.63        72.07 
TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A132 TCGA-C8-A134 
       26.14        57.83        18.64        11.93         1.87         1.12 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        4.08        11.28        12.03         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XB 
        0.43        14.17        18.90        12.03        20.12        18.15 
TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27T TCGA-E2-A10C 
       16.41        15.16        16.04        14.43        13.08        40.11 
TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A15F TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1IN 
       33.30        18.51        21.63        17.06        14.07        22.19 
TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A56Z TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI 
       27.42        18.87         8.28        12.59        35.24         9.86 
TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22B 
        2.56        40.24         6.58        21.27        34.13        22.75 
TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1P5 TCGA-EW-A1P8 
       12.89         1.94        23.84        14.70        23.11         7.86 
TCGA-EW-A1PA TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-OL-A5RW 
       18.90        69.30         2.60        22.26        12.36        36.36 
TCGA-OL-A66I TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG 
       23.47        86.96         0.16        13.12 

$`10P LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
       50.37        38.37        21.30        23.21        21.14        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F 
       29.79        31.73        20.19        23.61        29.56        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
        0.99        38.01        28.96        19.96        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C 
       12.00        19.04        13.02         0.99        27.02         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       55.43        36.99        38.79        26.04        50.70        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        13.71        18.67 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.33         0.23         0.33         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.28         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
       12.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        95.70        68.75        47.87        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L 
       61.87        70.39         0.53        17.79        24.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        73.64        74.79        86.66        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        63.62        62.14        33.73       160.90        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
       96.89        78.51        84.20         2.76        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       53.36        85.35        83.77        79.00        78.48        73.18 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM 
       58.92       143.21        20.25        62.86        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 
       38.17        40.54        54.74        16.04        20.45        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       176.98       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88        43.59       101.52       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       74.99       103.63        71.15        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.16        48.36        56.94 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       51.68        32.02        18.21        25.71        24.85        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        41.75        48.13        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HI 
       37.78        35.51        24.56        23.08        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93       113.82        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
      120.62       114.15        33.17        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       55.00       144.59        72.07        28.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
        8.94        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        3.16         2.24         1.05         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Z 
       11.34         0.16        10.42         2.30         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        19.20        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        12.03        14.01        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69        15.55        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        12.99        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.24        14.14        17.42        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        38.60        33.17        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        28.60        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       33.73        33.70        28.44        22.65         3.88        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        26.56        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       12.85        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       13.12        36.56        39.55        35.77        25.84        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       28.27        34.95         6.12         3.02         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI 
       32.09        32.09         1.12        34.65        34.59        35.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G 
       32.05        12.53        13.32        39.09        41.03        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       20.71        17.06         0.69        27.22         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        29.72         0.76        26.07        18.41        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       15.72        12.33         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        34.03        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12        62.43        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        14.79         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        14.70        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        16.50        16.93        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        15.35        14.96        13.84        13.94        17.03 
TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.03               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            139.17             234.28 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            22.045             24.970 
[1] "0.0 - 139.2 (22.0)" "0.0 - 234.3 (25.0)"
[1] "hr=" "1.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED        11        4        0        1        59        39
  10P LOSS WILD-TYPE      78       77        8        2       294       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1         32          6         11        3
  10P LOSS WILD-TYPE         1        118         23         52       17
                    vv
clus                 STAGE TIS STAGE X
  10P LOSS MUTATED           0       1
  10P LOSS WILD-TYPE         1      12
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  4                 77
  STAGE IB                  0                  8
  STAGE II                  1                  2
  STAGE IIA                59                294
  STAGE IIB                39                206
  STAGE III                 1                  1
  STAGE IIIA               32                118
  STAGE IIIB                6                 23
  STAGE IIIC               11                 52
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    26 114  18   9
  10P LOSS WILD-TYPE 246 502 112  31
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               26                246
  T2              114                502
  T3               18                112
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    69  57  26  12
  10P LOSS WILD-TYPE 432 293  91  63
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               69                432
  N1               57                293
  N2               26                 91
  N3               12                 63
[1] 4 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
  10P LOSS MUTATED   149   3
  10P LOSS WILD-TYPE 730  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    149    3
  10P LOSS WILD-TYPE  730   18
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              149                730
  1                3                 18
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   168   0
  10P LOSS WILD-TYPE 883  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    168    0
  10P LOSS WILD-TYPE  883   11
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              168                883
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P LOSS MUTATED                            0                           126
  10P LOSS WILD-TYPE                          1                           637
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P LOSS MUTATED                               19                   0
  10P LOSS WILD-TYPE                            173                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P LOSS MUTATED                       1                                8
  10P LOSS WILD-TYPE                     3                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10P LOSS MUTATED                    1             12
  10P LOSS WILD-TYPE                 16             36
D60V8, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 126                637
  INFILTRATING LOBULAR CARCINOMA                 19                173
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 22
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 12                 36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    45 123
  10P LOSS WILD-TYPE 243 651
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     45  123
  10P LOSS WILD-TYPE  243  651
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                45                243
  YES              123                651
[1] 2 2
[1] FALSE
D60V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0    12
  10P LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          21   116
  10P LOSS WILD-TYPE                       149   620
D60V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      21                149
  WHITE                                         116                620
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     3 135
  10P LOSS WILD-TYPE  35 723
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3  135
  10P LOSS WILD-TYPE   35  723
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              135                723
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   191  33
  10Q LOSS WILD-TYPE 725  95
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                820 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                33                 95 
$`10Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67         9.96        13.68        31.79        39.32 
TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       19.20        73.84        75.55        75.25         5.19       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0YE 
       67.33        25.22        27.12        17.52        49.84        18.21 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B 
       21.90        18.61        17.36        60.72        19.20        42.44 
TCGA-A2-A3XT TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ 
       83.01         7.30        24.39        26.96        21.90        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB 
       35.67        31.73        25.15        31.36        22.32        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06U 
       14.50        21.17        14.73        10.29        17.98        29.03 
TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I 
       53.98        14.01         8.98        15.06        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09R 
        9.99        43.00        12.00        12.00        49.05         8.98 
TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH 
       21.04        17.03        38.04         0.95         5.72        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
        0.92         2.27        17.42        13.58         0.03         1.12 
TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XN TCGA-AN-A0XP 
        7.36         0.33         0.33         0.36         0.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U 
        0.33         0.33         5.59        61.35        66.77        58.95 
TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12F TCGA-AQ-A04J 
       29.13        21.53        72.00       102.58        48.36        26.93 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 
       32.91        19.20         5.26        42.35        98.93        83.87 
TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 
       33.73        94.22       104.28        87.22        50.96        89.00 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO TCGA-AR-A2LR 
       72.76        93.83        54.21        66.15        39.39        20.38 
TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU 
       10.59        18.77       211.56        81.17       100.70       131.21 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV 
       73.51       139.17        74.99        68.12        24.53        59.84 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV 
       39.55        56.98        37.22        21.70        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0H9 
       11.67        49.05        44.02        24.49        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18T TCGA-BH-A18V 
       52.96        51.32        23.05         7.23         7.36        51.16 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FH 
       91.99        42.28        97.48        24.66       114.15        36.92 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12L 
       45.63        72.07        26.14        57.83        18.64        11.93 
TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HI 
       11.77        12.66         1.87         1.12         4.08        11.28 
TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.03         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JG 
       12.20        11.90        13.97        14.17        17.49        12.03 
TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XQ 
       20.12        18.58        18.15        15.22        21.83        16.41 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27T TCGA-E2-A10C 
       12.99        15.16        16.04        14.43        13.08        40.11 
TCGA-E2-A14N TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A159 TCGA-E2-A15F TCGA-E2-A15P 
       47.15        33.30        18.51        25.05        21.63        19.56 
TCGA-E2-A1IE TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LK 
       38.30        22.19        27.42        18.87       106.75         8.75 
TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 
        8.28        26.56        12.59        35.24         9.86         2.56 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E 
       40.24         6.58        21.27        34.13        22.75        12.89 
TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1OW TCGA-EW-A1OZ 
        1.94        29.72        23.84        14.70        22.82        40.41 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A2FV TCGA-GM-A2DC TCGA-GM-A3XL 
       23.11         7.86        18.90        25.91        83.34        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FP TCGA-LL-A7T0 
        2.60        11.84        11.57         7.10        22.26        12.36 
TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX 
       14.73        36.36        23.47        28.21        86.96         0.16 
TCGA-S3-A6ZG TCGA-S3-A6ZH 
       13.12        16.93 

$`10Q LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72       134.40        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13         8.38        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       32.55        25.28        50.47        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        31.73        23.77        23.47        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
      105.34        10.59        20.88        39.65        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        21.14        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        17.92        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 
       53.06        31.00        26.01         1.02        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        18.97        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       18.05        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       19.96        37.05        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
      112.08        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99         1.02        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 
       14.01        12.00        19.04        13.02         0.99        27.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       55.43        36.99        38.79        26.04        50.70        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55        11.44        13.71        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         9.96         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.28         7.04         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L 
        0.33        12.33         0.33         0.33         5.33        80.28 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 
       81.63        95.70        68.75        47.87        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      108.03        90.58        98.27        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TX 
        2.56       111.32        73.64        74.79        86.66        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       76.21        61.28        63.62        62.14       160.90        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
       96.89        78.51        84.20         2.76        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       53.36        85.35        83.77        79.00        78.48        73.18 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       58.92       143.21        20.25        62.86        52.11        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        54.74        16.04        20.45        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       176.98       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      110.93       140.88        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C 
       43.59       101.52       170.17        85.35       103.63        71.15 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       20.45        25.55        28.50        46.95        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       48.36        56.94        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       24.85        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       53.69        53.95        41.75        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB 
       10.78        15.16        37.78        35.51        24.56        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       44.81         8.81         2.01        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93       113.82        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       49.58        17.69        25.81        31.53        89.16       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       33.17        74.73       122.89        63.35        55.00       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       72.07        28.14        38.60        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28         8.94        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 
       12.66         0.39         3.16         2.24         1.05         4.11 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       12.33        10.92        11.34         0.16        10.42         2.30 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        20.58        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        16.50        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        18.97        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        14.50        19.92        17.69        15.55        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.24        14.14        17.42        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       40.41        37.51        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        13.02        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        17.10        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        20.98        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI 
       39.62        19.66        24.59        40.47        28.90       102.61 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
       43.04        16.93         5.52        15.72        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       12.00        13.12        36.56        39.55        35.77        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        28.27        34.95         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH 
       21.21        32.09        32.09         1.12        34.65        34.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       35.64        32.05        12.53        13.32        39.09        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 
       23.51        20.71        17.06         0.69        27.22         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56         0.72         0.76        26.07        18.41        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       15.72        12.33         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.43 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       21.24        13.22        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.79         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       14.70        14.07        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       58.52        31.99        58.62        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        17.36        14.07        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
        8.91        47.01        64.21         0.26         9.93        16.50 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.03               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            211.56             234.28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            22.225             25.005 
[1] "0.0 - 211.6 (22.2)" "0.0 - 234.3 (25.0)"
[1] "hr=" "1.5"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED        17        9        1        1        73        52
  10Q LOSS WILD-TYPE      72       72        7        2       280       193
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1         38          7         19        4
  10Q LOSS WILD-TYPE         1        112         22         44       16
                    vv
clus                 STAGE TIS STAGE X
  10Q LOSS MUTATED           0       2
  10Q LOSS WILD-TYPE         1      11
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                  9                 72
  STAGE IB                  1                  7
  STAGE II                  1                  2
  STAGE IIA                73                280
  STAGE IIB                52                193
  STAGE III                 1                  1
  STAGE IIIA               38                112
  STAGE IIIB                7                 22
  STAGE IIIC               19                 44
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    40 145  25  13
  10Q LOSS WILD-TYPE 232 471 105  27
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               40                232
  T2              145                471
  T3               25                105
  T4               13                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    96  73  32  20
  10Q LOSS WILD-TYPE 405 277  85  55
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               96                405
  N1               73                277
  N2               32                 85
  N3               20                 55
[1] 4 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
  10Q LOSS MUTATED   196   4
  10Q LOSS WILD-TYPE 683  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    196    4
  10Q LOSS WILD-TYPE  683   17
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              196                683
  1                4                 17
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   224   1
  10Q LOSS WILD-TYPE 827  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    224    1
  10Q LOSS WILD-TYPE  827   10
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              224                827
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q LOSS MUTATED                            0                           175
  10Q LOSS WILD-TYPE                          1                           588
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q LOSS MUTATED                               23                   1
  10Q LOSS WILD-TYPE                            169                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q LOSS MUTATED                       1                                8
  10Q LOSS WILD-TYPE                     3                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10Q LOSS MUTATED                    1             15
  10Q LOSS WILD-TYPE                 16             33
D61V8, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 175                588
  INFILTRATING LOBULAR CARCINOMA                 23                169
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 22
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 15                 33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    61 164
  10Q LOSS WILD-TYPE 227 610
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     61  164
  10Q LOSS WILD-TYPE  227  610
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                61                227
  YES              164                610
[1] 2 2
[1] FALSE
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0    18
  10Q LOSS WILD-TYPE                                1    42
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          43   142
  10Q LOSS WILD-TYPE                       127   594
D61V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                 42
  BLACK OR AFRICAN AMERICAN                      43                127
  WHITE                                         142                594
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3 186
  10Q LOSS WILD-TYPE  35 672
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3  186
  10Q LOSS WILD-TYPE   35  672
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              186                672
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   227  37
  11P LOSS WILD-TYPE 689  91
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               264                780 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                37                 91 
$`11P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CO 
        9.96        13.68        39.32        18.02        73.84       114.81 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0SX 
       56.81        34.55        79.76        74.40        35.05        50.43 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25B 
       17.13        21.90        18.61        23.77        60.72        42.44 
TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A7-A0CE TCGA-A7-A0DA 
      105.34        33.93        47.31        38.37        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A4SA TCGA-A7-A4SE 
       31.73        20.19        25.15        31.36        14.93        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 
       14.73        10.29        13.02        53.06         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G 
       43.00        14.01         9.99        18.05        33.01        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X 
       37.05         9.99        31.00         0.99        33.01        43.00 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09T 
       17.95        12.00        12.00        49.05        45.07        19.04 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       12.00        19.04        17.03         2.37        38.53        99.35 
TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A6IW TCGA-AC-A6IX 
       36.99        26.04        33.04        16.57        13.58        12.26 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS 
        0.03         1.12         0.23         2.96         6.51         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       61.35        95.70        20.32        53.03        21.53        50.70 
TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KS TCGA-AO-A1KT 
       55.33        57.30        48.36        41.62         0.53        17.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 
        2.56        32.91        86.66        42.35       107.24        65.36 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AU TCGA-AR-A1AW 
       83.87       114.02        85.97        51.25        76.21        63.62 
TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24Z TCGA-AR-A2LL TCGA-AR-A2LO 
      160.90        87.22        76.01        79.00        66.15        39.39 
TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RU 
       12.13        65.72       146.50        18.77       110.14       131.21 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KN 
       79.63        18.35        21.47       186.48       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B5 TCGA-BH-A0B6 
       74.99       103.63        59.84        25.55        48.36        56.94 
TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 
       37.22        18.21        44.05        48.69        49.94        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       44.02        48.13        42.90        22.13        13.91        48.23 
TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HX 
       31.00        10.78        15.16        23.08        52.96        27.25 
TCGA-BH-A0HY TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN 
       50.79        26.66        30.28        55.63         7.36        69.93 
TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A28Q 
      113.82        31.53        24.66       114.15        38.60         6.44 
TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       10.52        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG 
       12.66         1.87         1.05         4.08        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
       11.28        12.03        10.42         3.25         0.36         0.43 
TCGA-C8-A278 TCGA-C8-A8HQ TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 
        9.50        12.49        20.88        13.97        13.48        14.17 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 
       15.78        18.15        18.90        18.97        20.12        17.79 
TCGA-D8-A1XJ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27G 
       21.83        16.31        12.99        12.66        15.32        13.45 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14R 
       10.09        12.26        43.00        46.59        40.11        38.60 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       31.96        18.51        14.79        25.05        20.71        18.21 
TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       17.10        32.78        33.73        27.42        39.62        24.59 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A9RU 
      106.75       102.61         8.75        43.04        34.92        12.85 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1RF TCGA-E9-A1RG 
       13.12        36.56        12.59        35.24         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       34.59        35.64        12.53        22.75        41.03        12.89 
TCGA-E9-A22G TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OZ 
       23.51        26.07        30.18        13.81        14.40        40.41 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-GM-A2DI 
       29.82         7.86         6.15        14.43        55.00        85.15 
TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       85.35        69.30         7.10        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5RW 
       22.26        12.36        14.73        27.91        36.30        36.36 
TCGA-OL-A5RZ TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-PL-A8LX TCGA-S3-A6ZF 
       22.32        65.62        41.92        17.36         0.16        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       13.12        16.93        17.03        16.04       108.07       107.05 

$`11P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
       18.21       104.81        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        67.33        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EU 
      101.72       134.40        80.28       107.61        72.00        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 
       27.12        44.88        44.28        17.52         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       18.21        50.47        21.67        49.48        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.47        17.36        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        34.98        50.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13G 
       35.47        30.61        37.45        33.11        29.79        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        11.97        13.74        14.50        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 
        1.02        17.98        29.03        31.00        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       53.98        19.99        18.97        18.97        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99        24.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       12.00        31.00       112.08        40.01        33.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09K 
       41.98         9.99         9.99         1.02        50.04        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02         8.98        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD 
       14.01        13.02        21.04         0.99        27.02        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95        10.85         5.72         1.48        40.57        55.43 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        50.70         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83        22.19        14.99        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6NO 
        1.55        11.44        13.71        17.42        18.67         1.68 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        8.22        20.19         1.32         2.30         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         1.78         1.71         9.96         7.36 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FX TCGA-AN-A0FY 
        7.96         7.00         7.59         7.17         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        5.33         5.59        80.28        66.77        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       26.04        37.48        22.36        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 
       21.37        26.24        50.24        62.04        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       64.04        28.37        14.73        82.62        61.87        70.39 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW 
       19.20       111.32        73.64         5.26        74.79        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       64.83        55.86       101.95        75.55        61.84        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        76.11        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        61.28        62.14        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
       97.84        53.36        85.35        50.96        83.77        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       143.21 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       20.25        62.86        54.21        52.11        38.17        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH 
      143.38       149.59       220.90       129.57        50.70       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      176.98       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      162.05       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       97.48       188.68       113.79       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88        43.59        73.51       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
       68.12        71.15        24.53        20.45        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       40.83        39.55        39.16        56.98        51.68        32.02 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        24.85        21.70        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DD 
       53.69        53.95        45.57        11.67        49.05        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       31.17        23.44        38.01        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        24.43        30.35        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       36.85        12.89        51.32         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S 
       20.12        90.84        72.56        37.74        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        51.16        91.99        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 
       55.69        49.58        17.69        25.81        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 
       26.14        83.31        57.83       130.16        10.65        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O 
        9.70        18.87        21.76         9.44        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66         0.39         3.16         2.24         1.12 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
        4.11        12.33         0.16         2.30         0.30         0.23 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
        8.28         9.67         9.53         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.03         0.23        13.02        13.41        19.46        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        14.17        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       16.50        18.71        12.03        12.03        14.01        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       14.70        18.58        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       18.15        12.39        17.16        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       19.92        17.69        15.55        16.41        15.85         6.35 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       13.48         4.80         0.76        13.08        12.53        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 
       18.51        21.67        16.18         8.02        12.10        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       34.26        32.02        28.60        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       16.47        38.30        37.41        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
        3.88        22.19        20.98        11.08        54.18        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       40.47        28.90        18.87        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        26.56        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        13.48        12.00        39.55        35.77        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A 
        1.12        34.65        34.13        32.05        13.32        39.09 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       20.71        17.06         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56         0.72        29.72         0.76        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        23.84        14.70         0.79        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        19.99        13.94        10.52        34.55        19.96 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       23.51         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        70.85        72.10        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      106.06       101.62       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ 
       11.44        10.95        25.05        17.06        14.70         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 
       16.08        15.68         7.46        14.50        14.70        14.07 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
        8.91        47.01        64.21        86.96         0.26         9.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       13.94         3.81        11.41        52.96        29.03        15.35 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.03               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            186.48             234.28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            23.295             24.640 
[1] "0.0 - 186.5 (23.3)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.3"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        20       10        2        0        90        58
  11P LOSS WILD-TYPE      69       71        6        3       263       187
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         48         14         18        5
  11P LOSS WILD-TYPE         2        102         15         45       15
                    vv
clus                 STAGE TIS STAGE X
  11P LOSS MUTATED           1       2
  11P LOSS WILD-TYPE         0      11
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 10                 71
  STAGE IB                  2                  6
  STAGE II                  0                  3
  STAGE IIA                90                263
  STAGE IIB                58                187
  STAGE III                 0                  2
  STAGE IIIA               48                102
  STAGE IIIB               14                 15
  STAGE IIIC               18                 45
  STAGE IV                  5                 15
  STAGE TIS                 1                  0
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    56 162  32  18
  11P LOSS WILD-TYPE 216 454  98  22
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               56                216
  T2              162                454
  T3               32                 98
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED   117  85  41  20
  11P LOSS WILD-TYPE 384 265  76  55
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              117                384
  N1               85                265
  N2               41                 76
  N3               20                 55
[1] 4 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
  11P LOSS MUTATED   225   6
  11P LOSS WILD-TYPE 654  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    225    6
  11P LOSS WILD-TYPE  654   15
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              225                654
  1                6                 15
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   267   2
  11P LOSS WILD-TYPE 784   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    267    2
  11P LOSS WILD-TYPE  784    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE              267                784
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P LOSS MUTATED                            0                           204
  11P LOSS WILD-TYPE                          1                           559
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P LOSS MUTATED                               36                   4
  11P LOSS WILD-TYPE                            156                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P LOSS MUTATED                       1                               10
  11P LOSS WILD-TYPE                     3                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11P LOSS MUTATED                    3             11
  11P LOSS WILD-TYPE                 14             37
D62V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 204                559
  INFILTRATING LOBULAR CARCINOMA                 36                156
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                 11                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    77 192
  11P LOSS WILD-TYPE 211 582
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     77  192
  11P LOSS WILD-TYPE  211  582
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                77                211
  YES              192                582
[1] 2 2
[1] FALSE
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1    19
  11P LOSS WILD-TYPE                                0    41
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          57   163
  11P LOSS WILD-TYPE                       113   573
D62V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          19                 41
  BLACK OR AFRICAN AMERICAN                      57                113
  WHITE                                         163                573
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4 212
  11P LOSS WILD-TYPE  34 646
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4  212
  11P LOSS WILD-TYPE   34  646
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO              212                646
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   314  39
  11Q LOSS WILD-TYPE 602  89
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               353                691 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                39                 89 
$`11Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SJ 
      129.14        40.14         9.96        14.37        43.43        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T 
        7.96        39.32        18.21        18.02       121.94        73.84 
TCGA-A2-A04V TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX 
       63.12       136.73        24.79       114.81        75.25        56.81 
TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0SU 
       25.22        79.76        74.40        35.05        61.94        54.64 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC 
       50.43        17.13        49.84        20.52        20.75        32.55 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       50.47        49.48        19.33        23.77        17.36        60.72 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XX 
       42.44       105.34        20.88        39.65        33.93        47.31 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC 
       38.37         7.30        35.31        30.61        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3J1 
       31.73        20.19        25.15        29.56        31.36        11.28 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O 
       14.93        13.74        14.50        21.17        10.29        13.02 
TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W 
       53.06         1.02         9.01        43.00        14.01         9.99 
TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       18.05        33.01        19.96        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A097 
       31.00        33.01        43.00        33.01        17.95        12.00 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        8.98        19.04        12.00        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       27.02        17.03         0.95         2.37        38.53        99.35 
TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3W5 TCGA-AC-A6IV 
       36.99        26.04        33.04        16.31        16.57        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A041 
       13.58        12.26         0.03         1.12         0.33         0.23 
TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        2.96         6.51         6.28         7.04         0.33         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         0.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 
       61.35        95.70        47.87        21.40        20.32        53.03 
TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KS 
       21.53        26.24        55.33        57.30        48.36         0.53 
TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TV 
       17.79        15.62         2.56        32.91        86.66        42.35 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       101.95        83.87       114.02        85.97 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       61.84        51.25        76.11        76.21        61.28        63.62 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
      160.90        94.22        87.22        79.00        89.00        58.92 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG 
       54.21        66.15        39.39        12.13       129.57       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV 
       18.77       126.12        68.45        81.17       131.21        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
       18.35        21.47       186.48        58.88       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B5 
       74.99       103.63        24.53        25.55        28.50        48.36 
TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 
       37.22        18.21        44.05        48.69        49.94        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DK 
       44.02        48.13        42.90        45.83        31.17        13.91 
TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       48.23        14.30        31.00        24.43        10.78        15.16 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX 
       23.08        52.96        26.50        13.61        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A1EN TCGA-BH-A1ES 
       50.79        23.05        26.66        30.28        69.93       113.82 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12M 
       31.53        24.66         6.44        10.52        18.64        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 
       11.77        12.66        12.66        12.66         1.87         1.05 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
        4.08        10.92        11.34        11.28        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 
        3.25         0.23         0.36         0.43         8.28         9.50 
TCGA-C8-A27A TCGA-C8-A8HQ TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 
       12.20        12.49        20.88        13.97        13.48        14.17 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 
       15.78        18.15        18.90        18.97        20.12        17.79 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XZ 
       25.74        23.90        15.22        16.31        12.99        15.32 
TCGA-D8-A1Y0 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       15.52        13.45        14.43        10.09        12.53        12.26 
TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V 
       43.00        46.59        44.68        38.60        33.17        34.26 
TCGA-E2-A14X TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       31.96        21.04        14.79        25.05        20.71        18.21 
TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IU 
        9.04        11.05        17.10        32.78        33.73        11.08 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z 
       27.42        39.62        24.59         8.75        43.04         8.28 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.92        34.29        12.85        36.82        13.12        36.56 
TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       11.90        34.95        21.21         6.58        21.27        35.64 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A295 
       22.75        41.03        12.89        23.51        27.22         0.72 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1J1 
       26.07        30.18        13.81        14.40        12.20        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P4 
       13.25        16.57        15.68        29.85        40.41        29.82 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A423 
        6.15        13.94        14.43        55.00        52.73        10.16 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LD-A7W6 
       23.51        59.57        85.35        69.30         7.10        13.28 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ 
       15.32        14.47        14.79        22.26        16.08        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RW 
       12.36        14.73        27.91         2.10        58.62        36.36 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O 
       24.72        22.32        20.38        65.62        41.92        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
       14.07        28.21        47.01         0.16        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.93        13.94        16.04       108.07       107.05 

$`11Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
      131.67        42.81        11.44        48.56        48.36         8.52 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SO 
       48.10        14.27        47.24        20.88        31.79        28.01 
TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       19.20       104.81        78.41        87.25       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       36.13        99.12        92.48        88.60       107.93        75.55 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        98.99       107.93        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES 
       61.58       101.72       134.40        80.28       107.61        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       34.29        31.82        24.72        63.29        99.19        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.88        44.28        17.52         8.38        17.46        18.90 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YL 
       25.28        18.21        21.90        21.67        18.61        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       31.73        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F 
       16.47        52.47       107.70        17.19        18.15        10.59 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       83.01        29.98        32.75        49.48        34.98        50.37 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G 
       38.30        34.29        35.47        37.45        33.11        23.61 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        13.41        14.70        11.97 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U 
       10.42         8.75        13.02         1.02        17.98        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        17.03        53.98        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99        24.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08R TCGA-A8-A08T 
        0.99        38.01        28.96        12.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       40.01        30.97        41.98         9.99         9.99         1.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 
        1.02        25.02        15.02         0.99        14.01         0.99 
TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
       38.04        10.85         5.72         1.48        40.57        55.43 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3OD 
       38.79        50.70         0.92         2.27        32.45        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       22.19        14.99        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP 
       11.44        13.71        17.42         1.68         8.22        20.19 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        1.32         2.30         0.33         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.36         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        7.17         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         0.33         5.33        66.77        81.63        68.75 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       22.36        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G 
      106.78       108.03        90.58        98.27        64.04        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65        32.52        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       73.64         5.26        74.79        98.93        64.83        55.86 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       75.55        52.77        48.82        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       43.07        17.23        37.81        62.14        33.73        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       96.89        78.51        84.20         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       76.01        53.36        85.35        50.96        83.77        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        93.83       143.21        20.25        62.86 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       52.11        38.17        40.54        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO 
       50.70        65.72       112.37       176.98        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      110.93       140.88       211.56       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68       113.79       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       28.27        68.94        43.59        73.51       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B2 
       68.12        71.15        59.84        20.45        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        56.94        56.98        51.68        32.02 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        24.85        21.70        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DG 
       53.69        53.95        45.57        11.67        49.05        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       38.01        22.13        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY 
        9.63        44.81        46.19        32.58        24.49        30.35 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK 
       37.78        35.51        24.56        41.00        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
        2.50        36.85        51.32         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        37.74        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
        7.36        51.39        51.16        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       12.00        55.69        49.58        17.69        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07        28.14        26.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
      130.16        10.65        20.12       109.28         8.94        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Z 
       11.93        11.77        12.66        12.66        12.66         0.39 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ 
        3.16         2.24         1.12         4.11        12.33         0.16 
TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B 
        2.30         0.30         9.67         9.53         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.03         0.23        13.02        13.41        19.46        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        14.17        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       16.50        18.71        12.03        12.03        14.01        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       14.70        18.58        16.73        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        14.73        21.83        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       15.55        16.41        15.85         6.35        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       16.54         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       13.05         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       12.10        34.42        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14T 
       28.44        28.87        47.15        40.96        38.24        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       43.33        32.02        28.60        18.51        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.24        19.43        23.87        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15O 
       21.63        12.92        17.42        19.40        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        33.01        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       20.98        54.18        19.66        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      106.75       102.61        16.93         5.52        15.72        30.61 
TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
       26.56        34.82        32.88        13.48        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 
       12.59        35.77        35.24        25.84         9.86        28.27 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         6.12         3.02         2.76        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         1.12        34.65        34.59        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       12.53        13.32        39.09        20.71        17.06         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        1.94         7.13        24.56        29.72         0.76        18.41 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE 
       15.72        12.33        23.84        14.70         0.79        15.39 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       39.72         8.48        18.21        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.95        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PG 
       30.08         7.86        18.90        19.99        10.52        34.55 
TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-GI-A2C8 
       19.96        25.91        22.09        34.03        17.49         7.40 
TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.22        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       17.06        14.70         2.63        15.68         7.46        14.50 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU 
       14.07        22.39        36.30        58.52        31.99        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N 
       34.92        28.87        26.70        23.47        42.77        26.04 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY 
       19.73        40.11         8.91        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.84        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 
       15.35 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            186.48             234.28 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             23.51              24.79 
[1] "0.0 - 186.5 (23.5)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        22       21        3        1       117        86
  11Q LOSS WILD-TYPE      67       60        5        2       236       159
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           1         63         14         20        7
  11Q LOSS WILD-TYPE         1         87         15         43       13
                    vv
clus                 STAGE TIS STAGE X
  11Q LOSS MUTATED           0       4
  11Q LOSS WILD-TYPE         1       9
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  22                 67
  STAGE IA                 21                 60
  STAGE IB                  3                  5
  STAGE II                  1                  2
  STAGE IIA               117                236
  STAGE IIB                86                159
  STAGE III                 1                  1
  STAGE IIIA               63                 87
  STAGE IIIB               14                 15
  STAGE IIIC               20                 43
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of 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    79 219  43  18
  11Q LOSS WILD-TYPE 193 397  87  22
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               79                193
  T2              219                397
  T3               43                 87
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED   156 119  53  24
  11Q LOSS WILD-TYPE 345 231  64  51
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0              156                345
  N1              119                231
  N2               53                 64
  N3               24                 51
[1] 4 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
  11Q LOSS MUTATED   288   8
  11Q LOSS WILD-TYPE 591  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    288    8
  11Q LOSS WILD-TYPE  591   13
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              288                591
  1                8                 13
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   354   6
  11Q LOSS WILD-TYPE 697   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    354    6
  11Q LOSS WILD-TYPE  697    5
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE              354                697
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q LOSS MUTATED                            0                           259
  11Q LOSS WILD-TYPE                          1                           504
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q LOSS MUTATED                               68                   4
  11Q LOSS WILD-TYPE                            124                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q LOSS MUTATED                       1                               11
  11Q LOSS WILD-TYPE                     3                               19
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11Q LOSS MUTATED                    4             12
  11Q LOSS WILD-TYPE                 13             36
D63V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 259                504
  INFILTRATING LOBULAR CARCINOMA                 68                124
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 19
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                 12                 36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   103 257
  11Q LOSS WILD-TYPE 185 517
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    103  257
  11Q LOSS WILD-TYPE  185  517
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               103                185
  YES              257                517
[1] 2 2
[1] FALSE
D63V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1    23
  11Q LOSS WILD-TYPE                                0    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          73   224
  11Q LOSS WILD-TYPE                        97   512
D63V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          23                 37
  BLACK OR AFRICAN AMERICAN                      73                 97
  WHITE                                         224                512
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    12 278
  11Q LOSS WILD-TYPE  26 580
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  278
  11Q LOSS WILD-TYPE   26  580
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 26
  NOT HISPANIC OR LATINO              278                580
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED   120  21
  12P LOSS WILD-TYPE 796 107
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               141                903 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                107 
$`12P LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YF 
       20.88        13.68        34.55        17.52        20.75        50.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 
       52.47        42.44        17.19        83.01        47.31        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A26I 
       24.39        26.96        30.61        35.67        31.73        21.73 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A07G 
       14.93        17.92        10.29        17.98        53.06        18.97 
TCGA-A8-A08F TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A09I TCGA-A8-A09Q 
       33.01         0.99        43.00        40.01        45.07        25.02 
TCGA-AC-A23H TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A6IV TCGA-AC-A7VB TCGA-AC-A8OQ 
        5.72         0.92         2.27        18.67         8.22         1.12 
TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0XN 
        0.16         6.44         7.00         7.59         0.33         0.33 
TCGA-AN-A0XO TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A129 
       12.33        81.63        47.87        52.18        55.33       108.03 
TCGA-AO-A12D TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ 
       64.04         5.26       107.24        65.36        61.84        52.77 
TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       17.23        50.89        96.89        78.48        73.18        72.76 
TCGA-AR-A256 TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       93.83        66.15       146.50       112.37       176.98        18.77 
TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A1KF 
      211.56       234.28       102.77       131.21       157.41       101.52 
TCGA-B6-A1KN TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BW 
      139.17        40.83        39.55        56.98        48.69        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EE 
       41.75        42.90        23.44         3.22         9.63        31.00 
TCGA-BH-A0H7 TCGA-BH-A1EN TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 
       23.08        69.93        97.48        72.07        72.07        57.83 
TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A26Y 
       12.66         2.24         1.87         1.12        11.28         0.43 
TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1X5 TCGA-D8-A1XK 
       12.20        13.97        18.90        12.03        18.58        14.50 
TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A14Q 
       17.69        16.41         6.35        16.04        40.41        38.24 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1B5 
       18.51        25.41        21.04        25.05        20.71        32.35 
TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI 
       17.10        20.98        27.42        24.59       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1R4 TCGA-E9-A22G TCGA-E9-A3X8 
        8.75        34.92        12.85         6.12        23.51        15.72 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A3U0 
       13.81        14.40        29.85         6.15        13.94        17.49 
TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-OL-A5D7 
       86.96        15.32        14.79        16.08         7.46        58.52 
TCGA-OL-A5RW TCGA-OL-A66K TCGA-UU-A93S 
       36.36        41.92         3.81 

$`12P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        67.33        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        18.21        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       17.36        60.72        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.47       107.70        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       39.65        33.93        29.98        32.75        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
       50.37         7.30        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       11.05         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       53.98         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        38.01        28.96        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00        31.00        33.01       112.08 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
        9.99        12.00         1.02        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        99.35        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        26.04        50.70        33.04        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW 
       24.79         1.55        11.44        13.71        17.42        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         0.03        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        1.78         1.71         9.96         7.36         6.51         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         0.33         5.65         7.96         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        61.35        66.77        95.70        68.75 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        21.40        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       102.58        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
       32.91        19.20       111.32        73.64        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U2 
       42.35        98.93        64.83        55.86       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        75.55        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        43.07        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        63.62        62.14        33.73       160.90        94.22 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       78.51        84.20         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       89.00        58.92       143.21        20.25        62.86        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM 
       12.13       220.90       129.57        50.70        65.72       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       110.14       110.93       140.88        68.45       189.01 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       162.05       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       58.88        43.59        73.51       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       68.12       103.63        71.15        24.53        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        28.50        46.95        39.16        48.36        56.94 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        44.05        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        45.57        49.94        49.05        44.02        48.13 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        24.49        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       55.63        37.55        66.05         7.36        51.39        51.16 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        89.16        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       63.35        55.00        45.63       144.59        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28         8.94        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A137 
       12.66        12.66         0.39         3.16         1.05         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.08        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03         0.23        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       11.90        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       21.83        19.92        15.55        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        14.14        17.42        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18         8.02        12.10        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       34.26        32.02        31.96        28.60        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 
       14.99        60.53        53.62        53.03        33.01        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        22.19        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       39.62        19.66        40.47        28.90        18.87        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       16.93         5.52        15.72         8.28        30.61        26.56 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       34.29        34.82        32.88        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.03        12.89        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41        30.18        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.79        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       22.82        29.95        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       19.99        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       52.73        25.91        22.09        34.03        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        70.85        72.10        85.15       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.43 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 
       14.70        14.47        22.26         2.63        15.68        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        12.36        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       28.87        24.72        22.32        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        16.50        13.12        16.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       16.80        15.39        13.84        15.35        14.96        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       13.94        17.03        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            234.28             220.90 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             24.59              24.53 
[1] "0.2 - 234.3 (24.6)" "0.0 - 220.9 (24.5)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED        11        8        0        0        51        38
  12P LOSS WILD-TYPE      78       73        8        3       302       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         18         10          6        2
  12P LOSS WILD-TYPE         2        132         19         57       18
                    vv
clus                 STAGE TIS STAGE X
  12P LOSS MUTATED           0       1
  12P LOSS WILD-TYPE         1      12
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  8                 73
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                51                302
  STAGE IIB                38                207
  STAGE III                 0                  2
  STAGE IIIA               18                132
  STAGE IIIB               10                 19
  STAGE IIIC                6                 57
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    32  87  13  13
  12P LOSS WILD-TYPE 240 529 117  27
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               32                240
  T2               87                529
  T3               13                117
  T4               13                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    67  52  15   8
  12P LOSS WILD-TYPE 434 298 102  67
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               67                434
  N1               52                298
  N2               15                102
  N3                8                 67
[1] 4 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
  12P LOSS MUTATED   129   3
  12P LOSS WILD-TYPE 750  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    129    3
  12P LOSS WILD-TYPE  750   18
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0              129                750
  1                3                 18
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED   145   1
  12P LOSS WILD-TYPE 906  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    145    1
  12P LOSS WILD-TYPE  906   10
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE              145                906
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P LOSS MUTATED                            0                           127
  12P LOSS WILD-TYPE                          1                           636
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P LOSS MUTATED                                8                   2
  12P LOSS WILD-TYPE                            184                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P LOSS MUTATED                       0                                3
  12P LOSS WILD-TYPE                     4                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12P LOSS MUTATED                    1              5
  12P LOSS WILD-TYPE                 16             43
D64V8, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 127                636
  INFILTRATING LOBULAR CARCINOMA                  8                184
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  5                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    44 102
  12P LOSS WILD-TYPE 244 672
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     44  102
  12P LOSS WILD-TYPE  244  672
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                44                244
  YES              102                672
[1] 2 2
[1] FALSE
D64V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     8
  12P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          32    94
  12P LOSS WILD-TYPE                       138   642
D64V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      32                138
  WHITE                                          94                642
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3 123
  12P LOSS WILD-TYPE  35 735
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3  123
  12P LOSS WILD-TYPE   35  735
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              123                735
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED   102  20
  12Q LOSS WILD-TYPE 814 108
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               122                922 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                108 
$`12Q LOSS MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A3XS 
       48.10        13.68        34.55        17.52        18.21        33.93 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ 
       83.01        47.31        38.37        24.39        26.96        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       35.67        31.73        20.19        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A07G TCGA-A8-A08F 
       17.92        10.29         9.37        10.42        18.97        33.01 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09Q TCGA-AC-A2QJ TCGA-AC-A7VB TCGA-AC-A8OQ 
        0.99        43.00        25.02         2.27         8.22         1.12 
TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0XO TCGA-AO-A0J4 
        1.78         0.16         7.00         7.59        12.33        52.18 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0U0 TCGA-AR-A1AI 
       55.33       102.58       108.03        48.36        65.36        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-AR-A252 
       52.77        43.07        17.23        50.89        78.48        73.18 
TCGA-AR-A256 TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RE 
       93.83        66.15       146.50       112.37       176.98       211.56 
TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 
      234.28       102.77       131.21       101.52       139.17        74.99 
TCGA-BH-A0AV TCGA-BH-A0B2 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C7 
       59.84        40.83        56.98        48.69        41.75        42.90 
TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EE TCGA-BH-A18V TCGA-BH-A1EN 
       23.44         3.22         4.41        31.00        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A5IZ 
       91.99        97.48        72.07        72.07        57.83        18.64 
TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A142 
       12.66         2.24         1.87         0.43        12.20        13.97 
TCGA-D8-A143 TCGA-D8-A1JG TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A27F TCGA-E2-A10A 
       14.17        12.03        14.50        16.41        16.04        40.41 
TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD 
       25.41        25.05        20.71        60.53        32.35        17.10 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 
       20.98        27.42       106.75       102.61         8.75        16.93 
TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UP 
       34.92        12.85        21.27        23.51        15.72        14.40 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DK 
       29.82         7.86         6.15        17.49         7.40        86.96 
TCGA-LL-A5YP TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
       14.79         7.46        58.52        36.36        20.38        41.92 
TCGA-OL-A6VO TCGA-UU-A93S 
       28.21         3.81 

$`12Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        43.43        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        67.33        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.47        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU 
       18.15       105.34        10.59        20.88        39.65        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       32.75        49.48        34.98        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       29.56        31.36        24.26        23.74        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.70        11.97        13.74        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        11.05         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G 
       36.95        13.02         0.99        38.01        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       12.00        37.05         9.99        31.00        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
      112.08        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       49.05        45.07        29.98        33.07         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        27.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         5.72         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70        33.04         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         0.03        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         5.65         7.96         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        21.40        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        50.24        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       106.78        90.58        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       73.64         5.26        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       85.97        75.55        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.56        39.98        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        33.73       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        58.92       143.21        20.25        62.86        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       52.11        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IK 
       12.13       220.90       129.57        50.70        65.72        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      126.12        84.59       110.14       110.93       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      189.01        81.17        78.02       172.96       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       18.35        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        68.12       103.63        71.15        24.53        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        28.50        46.95        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       24.85        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       44.02        48.13        45.83        31.17        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        48.23        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        47.41        16.27        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        24.49        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
        7.36        51.39       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        45.63       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28         8.94        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         0.39         3.16         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50         0.99         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        11.90        20.88        13.25        20.58 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        21.83        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       15.55        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 
       34.26        32.02        31.96        28.60        18.51        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       23.24        19.43        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58        11.05        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        53.62        53.03        33.01 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        16.47        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       18.87        43.04         5.52        15.72         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       26.56        34.29        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.24        25.84         9.86        11.90        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       32.09        40.24         1.12        34.65         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        41.03        12.89        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         7.13        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        26.07        18.41        30.18        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70         0.79        13.81        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        23.51       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL 
       83.34        75.02        70.85        72.10        85.15       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.43        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.47        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       16.08        15.68        14.50        14.70        12.36        14.73 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       14.07        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        23.47        65.62        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        16.50        13.12 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.93        16.80        15.39        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.84        13.94        17.03        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.16               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            234.28             220.90 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            27.815             23.915 
[1] "0.2 - 234.3 (27.8)" "0.0 - 220.9 (23.9)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         9        6        0        0        45        36
  12Q LOSS WILD-TYPE      80       75        8        3       308       209
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         11          8          7        2
  12Q LOSS WILD-TYPE         2        139         21         56       18
                    vv
clus                 STAGE TIS STAGE X
  12Q LOSS MUTATED           0       1
  12Q LOSS WILD-TYPE         1      12
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  6                 75
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                45                308
  STAGE IIB                36                209
  STAGE III                 0                  2
  STAGE IIIA               11                139
  STAGE IIIB                8                 21
  STAGE IIIC                7                 56
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    25  79  10  11
  12Q LOSS WILD-TYPE 247 537 120  29
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               25                247
  T2               79                537
  T3               10                120
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    64  42  10   8
  12Q LOSS WILD-TYPE 437 308 107  67
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               64                437
  N1               42                308
  N2               10                107
  N3                8                 67
[1] 4 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
  12Q LOSS MUTATED   110   2
  12Q LOSS WILD-TYPE 769  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    110    2
  12Q LOSS WILD-TYPE  769   19
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0              110                769
  1                2                 19
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   126   0
  12Q LOSS WILD-TYPE 925  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    126    0
  12Q LOSS WILD-TYPE  925   11
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE              126                925
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q LOSS MUTATED                            0                           108
  12Q LOSS WILD-TYPE                          1                           655
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q LOSS MUTATED                                7                   3
  12Q LOSS WILD-TYPE                            185                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q LOSS MUTATED                       0                                1
  12Q LOSS WILD-TYPE                     4                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12Q LOSS MUTATED                    0              7
  12Q LOSS WILD-TYPE                 17             41
D65V8, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 108                655
  INFILTRATING LOBULAR CARCINOMA                  7                185
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  7                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    38  88
  12Q LOSS WILD-TYPE 250 686
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     38   88
  12Q LOSS WILD-TYPE  250  686
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                38                250
  YES               88                686
[1] 2 2
[1] FALSE
D65V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     6
  12Q LOSS WILD-TYPE                                1    54
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          35    79
  12Q LOSS WILD-TYPE                       135   657
D65V11, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 54
  BLACK OR AFRICAN AMERICAN                      35                135
  WHITE                                          79                657
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3 108
  12Q LOSS WILD-TYPE  35 750
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3  108
  12Q LOSS WILD-TYPE   35  750
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 35
  NOT HISPANIC OR LATINO              108                750
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   359  58
  13Q LOSS WILD-TYPE 557  70
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               417                627 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                58                 70 
$`13Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A1-A0SJ 
      129.14       131.67        14.37        43.43        20.88        13.68 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        19.20        18.21        18.02        78.41 
TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CS TCGA-A2-A0CT 
       87.25        55.43        24.79       114.81        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SV 
       25.22        80.28        74.40        34.29        31.82        27.12 
TCGA-A2-A0SW TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YM 
       44.88        20.75        18.21        49.48        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A3XT TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3Y0 
       23.77        23.47        83.01        49.48        47.31        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
        7.30        24.39        26.96        21.14        38.30        30.61 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I 
       29.79        31.73        25.15        31.36        23.74        21.73 
TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV 
       22.32        10.59        14.93        14.50        17.92        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       29.03        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 
       18.97        32.05         9.99        10.98         9.99        36.95 
TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       13.02        38.01        33.01        12.00         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B 
       31.00        33.01        43.00        30.97         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X 
       45.07        29.98        33.07         1.02        25.02        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BK 
       19.04        13.02        27.02        38.04         2.37        38.53 
TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 
       99.35        33.04         2.27        32.45        16.57        19.79 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.71        17.42        13.58         8.22         0.03        20.19 
TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         2.96         1.78         1.71         9.96 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        0.33         0.33         6.28         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N 
        0.33         0.33         5.33         5.59        80.28        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JE 
       81.63        68.75        21.40        52.18        37.48        76.77 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 
       50.24        62.04        55.33        71.80       102.58       108.03 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       57.30        48.36        41.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O 
       17.79        24.79       130.09        15.62         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TZ 
       19.20       111.32         5.26        42.35        64.83       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36        83.87        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       51.25        17.23        63.62        33.73        50.89        94.22 
TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
       78.51       104.28        97.84        76.01        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK 
       79.00        78.48        73.18        58.92        93.83        54.21 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IE 
       66.15        54.74        10.59        77.62       129.57        65.72 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RU 
      140.88        68.45        81.17       102.77       140.48       131.21 
TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X5 TCGA-B6-A1KC 
       97.48        79.63        18.35        21.47        68.94        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
      101.52        73.51       139.17       170.17        85.35        68.12 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B7 
       59.84        25.55        28.50        39.55        56.94        56.98 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV 
       37.22        32.02        21.70        48.69        53.69        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        41.75        44.02        42.90        45.83 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E0 TCGA-BH-A0E9 
       38.01        13.91        48.23        15.65         4.41        46.19 
TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HU 
       31.00        10.78        15.16        23.08        26.50        12.89 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L 
       27.25         5.59        23.93        23.05        90.84        26.66 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU 
       55.63        66.05         7.36        51.39        69.93        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FD 
       12.00        17.69        25.81        97.48       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A209 
       74.73        36.92        63.35        72.07        26.14       130.16 
TCGA-BH-A28Q TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12O 
        6.44        23.51         9.63         9.70        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG 
       11.77        12.66         3.16         1.05        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X 
       11.28        12.03         2.30         3.25         0.30         0.36 
TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Y 
        0.43         9.53         9.50         0.23        13.41        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        13.97        14.17        13.48        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        15.78        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JT 
       12.03        18.97        20.12        20.09        19.40        13.32 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XK 
       18.58        17.79        23.90        27.58        17.16        14.50 
TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       19.92        12.99        16.54        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27N TCGA-D8-A27T TCGA-E2-A107 TCGA-E2-A10C 
       14.14        14.43         4.80        13.08        34.42        40.11 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A155 
       47.15        44.68        32.02        25.41        27.12        21.04 
TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       25.05        18.21        11.05        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 
       14.07        60.53        33.70        22.19        20.98        39.62 
TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A576 
       18.87         8.75        43.04        16.93         8.28        34.29 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1R6 
       13.48        13.12        36.56        35.77         9.86         2.76 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A22E TCGA-E9-A22G 
       32.09        32.09         1.12        21.27        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A54Y 
       20.71        27.22         7.13         0.72        30.18        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1OV TCGA-EW-A1OW 
       13.81        14.40        15.39        12.20        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.85        40.41        52.96        23.11         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-GM-A2DB 
        6.15        14.43        19.96        52.73        17.49        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DL TCGA-GM-A3NW 
       83.34        75.02        70.85        72.10       115.69       110.50 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A5YM TCGA-LL-A5YO 
       69.30         2.60        21.24        13.22        15.32        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D7 
       14.79        22.26        16.08        14.70        12.36        58.52 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K 
       58.62        36.36        22.32        20.38        23.47        41.92 
TCGA-OL-A66N TCGA-OL-A66O TCGA-PE-A5DD TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA14 
       26.04        17.36        64.21        16.93        15.39        14.96 
TCGA-UL-AAZ6 TCGA-XX-A89A TCGA-Z7-A8R5 
       17.03        16.04       108.07 

$`13Q LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
        8.52        48.10        14.27        47.24        31.79         7.96 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      104.81       121.94        73.84        63.12       101.98        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0D2 
      136.73        99.12        92.48        88.60       107.93        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ES 
       61.58       101.72       134.40       107.61        79.76        72.00 
TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A1FW TCGA-A2-A1FX 
       21.90        21.67        18.61        19.33        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XY 
       20.88        39.65        33.93        29.98        32.75        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       50.37        21.30        23.21        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       35.47        37.45        35.67        33.11        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 
       29.56        24.26        23.80        20.61        11.34        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE 
       11.28        13.41        14.70        11.97        13.74        21.17 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q 
       14.73        12.10        10.72        11.05        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       31.00        17.03        19.99        18.97        14.01        12.00 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        8.98         7.99        24.99        45.07        18.05        15.06 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08R TCGA-A8-A08T 
        0.99        28.96        19.96        37.05         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
       40.01        33.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
        1.02        50.04        49.05         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A23C 
        0.99        12.00        21.04         0.99        17.03         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       10.85         5.72         1.48        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        26.04        50.70         0.92        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       22.19        14.99        23.24        24.79         1.55        11.44 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
       18.67        12.26         1.68         1.12         1.32         2.30 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.23         0.62         7.36         6.51         0.16 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO 
        7.17         7.04         0.33         0.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P 
        0.30         0.33         0.33         0.33        61.35        95.70 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        58.95        29.13        32.78        26.04        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       21.37        26.24        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04J 
       98.27        64.04        28.37        14.73        82.62        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
        5.65        32.52        73.64        74.79        86.66        98.93 
TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.86       101.95       114.02        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        43.07        37.81        76.21        61.28 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       62.14       160.90        96.89        84.20         2.76        87.22 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       53.36        83.77        89.00        72.76       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       62.86        52.11        38.17        39.39        40.54        20.38 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        20.45       143.38       149.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93       211.56       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       172.96       162.05       100.70        89.46       157.41 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X7 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       58.88        74.99       103.63        71.15        24.53        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BD 
       46.95        40.83        39.16        48.36        51.68        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        24.85        44.05        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       53.95        45.57        48.13        31.17        23.44        22.13 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26         3.22         2.56        38.47        67.86        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27        15.68        14.30         9.63        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        24.43        30.35        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        51.32        50.79        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
        8.81         2.01         7.23        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       30.28        37.55        51.16        91.99       113.82        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       55.69        49.58        31.53        89.16        24.66       120.62 
TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
      122.89        55.00        45.63        72.07       144.59        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        83.31        57.83        10.65        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
      109.28         8.94        18.64         5.26        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W 
        9.44        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66         0.39         2.24         1.87         1.12         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26W TCGA-C8-A26Z 
        4.08        12.33         0.16        10.42         0.23         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP 
        9.67         0.03        12.20         0.99         0.03        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A141 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF 
       12.49        19.46        20.58        19.20        18.71        12.03 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU 
       14.01        20.09        20.38        21.01        12.20        14.70 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       16.73        25.74        18.15        12.39        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        17.69        15.55        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F 
        6.35        15.16        12.66        15.32        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P 
       13.45        13.05         9.44        16.41        13.48         0.76 
TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        12.53        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       16.18         8.02        12.10        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q 
       40.41        37.51        28.44        28.87        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        34.26        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 
       28.60        18.51        23.24        19.43        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15T TCGA-E2-A1B0 
       17.42        19.40         9.04        20.58        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        33.01        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
        3.88        11.08        54.18        27.42        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P6 TCGA-E2-A3DX 
       40.47        28.90       106.75       102.61         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        26.56        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG 
       36.82        12.00        39.55        12.59        35.24        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI 
       21.21        40.24        34.65         6.58        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13        32.05        12.53        13.32        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS 
       41.03        17.06         0.69         1.94        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
        0.76        26.07        18.41        15.72        12.33        14.70 
TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
        0.79        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        15.68        28.77        29.95        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       29.82        18.48        30.08        19.99        13.94        10.52 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       34.55        55.00        25.91        22.09        34.03        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DI 
       23.51         7.40       109.87        59.57       216.76        85.15 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG 
       86.96       106.06       101.62        85.35        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       11.57         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y 
       10.95        25.05        17.06        14.70         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        2.10        36.30        31.99        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VO 
       24.72        26.70        65.62        42.77        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73        40.11         8.91        47.01        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         9.93        16.50        13.12        16.80        13.84 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       15.35        13.84        13.94         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       29.03        15.35       107.05 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            170.17             234.28 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             24.79              24.49 
[1] "0.0 - 170.2 (24.8)" "0.0 - 234.3 (24.5)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        33       27        3        1       155        99
  13Q LOSS WILD-TYPE      56       54        5        2       198       146
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1         60         11         22        7
  13Q LOSS WILD-TYPE         1         90         18         41       13
                    vv
clus                 STAGE TIS STAGE X
  13Q LOSS MUTATED           1       4
  13Q LOSS WILD-TYPE         0       9
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  33                 56
  STAGE IA                 27                 54
  STAGE IB                  3                  5
  STAGE II                  1                  2
  STAGE IIA               155                198
  STAGE IIB                99                146
  STAGE III                 1                  1
  STAGE IIIA               60                 90
  STAGE IIIB               11                 18
  STAGE IIIC               22                 41
  STAGE IV                  7                 13
  STAGE TIS                 1                  0
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of 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    94 259  56  16
  13Q LOSS WILD-TYPE 178 357  74  24
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               94                178
  T2              259                357
  T3               56                 74
  T4               16                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED   208 135  49  27
  13Q LOSS WILD-TYPE 293 215  68  48
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              208                293
  N1              135                215
  N2               49                 68
  N3               27                 48
[1] 4 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
  13Q LOSS MUTATED   353   8
  13Q LOSS WILD-TYPE 526  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    353    8
  13Q LOSS WILD-TYPE  526   13
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              353                526
  1                8                 13
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   422   5
  13Q LOSS WILD-TYPE 629   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    422    5
  13Q LOSS WILD-TYPE  629    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              422                629
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q LOSS MUTATED                            0                           337
  13Q LOSS WILD-TYPE                          1                           426
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q LOSS MUTATED                               56                   5
  13Q LOSS WILD-TYPE                            136                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q LOSS MUTATED                       1                               10
  13Q LOSS WILD-TYPE                     3                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  13Q LOSS MUTATED                    2             15
  13Q LOSS WILD-TYPE                 15             33
D66V8, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 337                426
  INFILTRATING LOBULAR CARCINOMA                 56                136
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 15                 33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   123 304
  13Q LOSS WILD-TYPE 165 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    123  304
  13Q LOSS WILD-TYPE  165  470
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               123                165
  YES              304                470
[1] 2 2
[1] FALSE
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0    24
  13Q LOSS WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          80   275
  13Q LOSS WILD-TYPE                        90   461
D66V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                 36
  BLACK OR AFRICAN AMERICAN                      80                 90
  WHITE                                         275                461
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11 334
  13Q LOSS WILD-TYPE  27 524
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  334
  13Q LOSS WILD-TYPE   27  524
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 27
  NOT HISPANIC OR LATINO              334                524
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   217  39
  14Q LOSS WILD-TYPE 699  89
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               256                788 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                 89 
$`14Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T 
      129.14        42.81        31.79        19.20        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ 
       87.25       101.98         5.19       107.93        67.33        79.76 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YJ 
       35.05        34.29        27.12        50.43        18.21        18.61 
TCGA-A2-A0YT TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       23.77        19.20        33.93        83.01        29.98        47.31 
TCGA-A2-A3Y0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D TCGA-A7-A13E 
       38.37        26.96        21.90        35.31        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SB 
       25.15        23.74        21.73        22.32        11.28        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.50        21.17        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O 
       13.02        31.00         1.02        18.97        32.05         9.99 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A097 
        8.98         9.99        33.01        19.96         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A23C 
       45.07        29.98         1.02        21.04        17.03         0.95 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW 
       38.53        99.35        33.04         2.27        13.71        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FJ TCGA-AN-A0FX 
        0.03         1.12         1.78         7.36         7.96         0.33 
TCGA-AN-A0XN TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 
        0.33        52.18        37.48        55.33       102.58       108.03 
TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       48.36        70.39       130.09         5.65         2.56        32.91 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AH TCGA-AR-A1AI 
        5.26        86.66        42.35        65.36        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AX TCGA-AR-A1AY 
       52.77        76.11        39.98        43.07        62.14        33.73 
TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 
      160.90       104.28        85.35        78.48        58.92        93.83 
TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
       12.13       112.37       176.98       110.14       140.88       211.56 
TCGA-B6-A0RL TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A1KF 
       81.17        97.48        18.35        21.47        43.59       101.52 
TCGA-B6-A1KI TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B5 
       73.51        24.53        59.84        20.45        39.55        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW 
       56.98        51.68        25.71        24.85        21.70        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0H7 
       49.05        44.02        42.90         4.41         9.63        23.08 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U 
        5.59        23.05         8.81        55.63         7.36        51.39 
TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE 
       55.69        17.69        97.48        24.66       114.15        74.73 
TCGA-BH-A202 TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12X 
       26.14        10.52        18.64        11.93        11.77        12.66 
TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Y 
        1.12        10.92        12.03         2.30         3.25         0.43 
TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JG 
        0.99        13.02        19.46        13.97        15.78        12.03 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XB 
       20.09        20.09        19.40        21.01        27.58        18.15 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY 
       14.73        14.50        15.55         6.35        12.99        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27T 
       15.52        14.14        14.43        13.48        10.09        13.08 
TCGA-E2-A108 TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 
       27.52        38.60        33.30        18.51        25.41        21.04 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1AZ 
       25.05        23.34        21.63        11.05        19.56        60.53 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z 
       33.73        33.70        28.90       106.75       102.61         8.28 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1QZ 
       34.92        26.56        13.48        12.00        13.12        11.90 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A22A TCGA-E9-A22B 
        6.12         3.02         2.76        32.09        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1J6 
       23.51        29.72        26.07        30.18        18.21        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PF TCGA-EW-A1PH 
       25.94        22.82        29.82         7.86        14.43        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 
       55.00        25.91        17.49        10.16        23.51       109.87 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A3XL TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YX 
       72.10        86.96        69.30        18.12         2.60        11.57 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RZ 
        7.10        11.44        14.79        12.36        58.52        22.32 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-PE-A5DC 
       20.38        23.47        41.92        26.04        28.21        47.01 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA17 TCGA-UL-AAZ6 
        0.16        16.50        16.80        15.39        13.94        17.03 
TCGA-UU-A93S TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        52.96        15.35        16.04 

$`14Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      104.81        78.41       121.94        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
      107.93        75.55        75.25        98.99        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        61.58        25.22       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
      107.61        74.40        72.00        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       63.29        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        31.73        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        39.65        32.75        49.48        34.98        50.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30        24.39        21.30        23.21        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       29.79        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        11.34        10.59        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       11.05        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        14.01        12.00        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
       38.01        28.96        12.00        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        17.95        41.98         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
        1.02        50.04        49.05        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
       13.02         0.99        27.02        38.04         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        5.72         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        50.70         0.92        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        14.99        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55        11.44        17.42        18.67        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        8.22        20.19         1.32         2.30         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        0.33         0.36         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       62.04        71.80        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        64.04        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87         0.53        17.79        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       15.62        32.52        19.20       111.32        73.64        74.79 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86       107.24       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      114.02        85.97        51.25        48.82        43.73        43.56 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K 
       17.23        37.81        76.21        61.28        63.62        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22        96.89        78.51        84.20         2.76        87.22 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84        76.01        53.36        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       89.00        73.18        72.76       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RG 
      146.50        18.77       126.12        84.59       110.93        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      189.01       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT 
      140.48       100.70        89.46       131.21       157.41       188.68 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       79.63       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       68.94        58.88       139.17       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       68.12       103.63        71.15        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       40.83        39.16        56.94        37.22        32.02        18.21 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD 
       53.95        45.57        49.94        41.75        48.13        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       47.41        16.27        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       42.35        44.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.16        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       12.00        49.58        25.81        31.53        89.16       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59        72.07        28.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       57.83       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
        8.94        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       21.76         9.44        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG 
        1.87         1.05         4.11         4.08        12.33        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       11.28         0.16        10.42         0.30         0.23         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        12.20 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.23        12.49        13.41        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        18.71        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS 
       12.03        14.01        18.97        20.12        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL 
       23.90        12.39        17.16        15.22        21.83        19.92 
TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW 
       17.69        16.41        15.85        16.31        15.16        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.32         9.93        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V 
       13.05         9.44        16.41         4.80         0.76        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       12.10        43.00        34.42        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.24        33.17        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 
       28.60        27.12        23.24        19.43        23.87        14.79 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S 
       19.40         9.04        20.58        13.02        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       16.47        17.10        38.30        37.41        32.78        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       27.42        39.62        19.66        24.59        40.47        18.87 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
        8.75        43.04        16.93         5.52        15.72        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA 
       34.29        12.85        34.82        32.88        36.82        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       39.55        12.59        35.77        35.24        25.84         9.86 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
       28.27        34.95         2.56        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E 
       34.13        32.05        12.53        13.32        41.03        12.89 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       20.71        17.06         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       24.56         0.72         0.76        18.41        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72         8.48        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        23.11        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW 
        6.15        13.94        10.52        34.55        52.73        22.09 
TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       34.03         7.40        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       75.02        70.85        85.15       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        62.43        11.84        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       10.62        24.95        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        14.70        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J 
       34.92        36.36        28.87        24.72        26.70        65.62 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       42.77        17.36        14.07        19.73        40.11         8.91 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       64.21        86.96         0.26         9.93        13.12        16.93 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-WT-AB44 
       13.84        15.35        14.96        13.84        11.41        29.03 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.03               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            211.56             234.28 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            22.785             24.970 
[1] "0.0 - 211.6 (22.8)" "0.0 - 234.3 (25.0)"
[1] "hr=" "1.5"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED        19       20        0        1        93        63
  14Q LOSS WILD-TYPE      70       61        8        2       260       182
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         34          5         15        6
  14Q LOSS WILD-TYPE         2        116         24         48       14
                    vv
clus                 STAGE TIS STAGE X
  14Q LOSS MUTATED           0       4
  14Q LOSS WILD-TYPE         1       9
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 20                 61
  STAGE IB                  0                  8
  STAGE II                  1                  2
  STAGE IIA                93                260
  STAGE IIB                63                182
  STAGE III                 0                  2
  STAGE IIIA               34                116
  STAGE IIIB                5                 24
  STAGE IIIC               15                 48
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of 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    52 172  27   8
  14Q LOSS WILD-TYPE 220 444 103  32
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               52                220
  T2              172                444
  T3               27                103
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED   138  74  29  16
  14Q LOSS WILD-TYPE 363 276  88  59
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              138                363
  N1               74                276
  N2               29                 88
  N3               16                 59
[1] 4 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
  14Q LOSS MUTATED   212   6
  14Q LOSS WILD-TYPE 667  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    212    6
  14Q LOSS WILD-TYPE  667   15
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              212                667
  1                6                 15
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   260   1
  14Q LOSS WILD-TYPE 791  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    260    1
  14Q LOSS WILD-TYPE  791   10
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE              260                791
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q LOSS MUTATED                            0                           212
  14Q LOSS WILD-TYPE                          1                           551
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q LOSS MUTATED                               27                   5
  14Q LOSS WILD-TYPE                            165                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q LOSS MUTATED                       2                                3
  14Q LOSS WILD-TYPE                     2                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  14Q LOSS MUTATED                    1             10
  14Q LOSS WILD-TYPE                 16             38
D67V8, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 212                551
  INFILTRATING LOBULAR CARCINOMA                 27                165
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 10                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    77 184
  14Q LOSS WILD-TYPE 211 590
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     77  184
  14Q LOSS WILD-TYPE  211  590
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                77                211
  YES              184                590
[1] 2 2
[1] FALSE
D67V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0    14
  14Q LOSS WILD-TYPE                                1    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          65   159
  14Q LOSS WILD-TYPE                       105   577
D67V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          14                 46
  BLACK OR AFRICAN AMERICAN                      65                105
  WHITE                                         159                577
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11 209
  14Q LOSS WILD-TYPE  27 649
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11  209
  14Q LOSS WILD-TYPE   27  649
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 27
  NOT HISPANIC OR LATINO              209                649
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   269  42
  15Q LOSS WILD-TYPE 647  86
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               311                733 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                42                 86 
$`15Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q 
       42.81        20.88        28.01        19.20        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS 
       73.84        87.25       101.98        99.12        24.79        75.55 
TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EO 
       75.25       107.93        56.81        67.33       134.40        80.28 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       79.76        35.05        63.29        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52        20.75        18.21        18.61        31.73 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW 
       19.20        33.93        29.98        47.31        38.37         7.30 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       26.96        21.90        30.61        35.67        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 
       20.19        31.36        24.26        21.73        22.32        11.28 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.50        17.92        14.73        10.29         9.37        10.42 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B 
       17.98        29.03        26.01         1.02        53.98        43.00 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       18.97         8.98        15.06        12.00         9.99        31.00 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09N 
       43.00        30.97        17.95         9.99         1.02         1.02 
TCGA-A8-A09W TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A2QJ 
        0.99        17.03         2.37        38.53        26.04         2.27 
TCGA-AC-A3OD TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A04A TCGA-AN-A0AJ 
       14.83        13.71        13.58        20.19         2.96         9.96 
TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV 
        7.36         0.33         6.44         7.00         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XS TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J6 TCGA-AO-A0J7 
        0.33        80.28        61.35        29.13        37.48        20.32 
TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KQ 
       53.03        72.00        55.33       108.03        48.36        61.87 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR 
        0.53        17.79        24.79         2.56        32.91         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       86.66        42.35        64.83        55.86        65.36       101.95 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AW 
       75.55        61.84        52.77        43.07        17.23        63.62 
TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W 
       33.73       104.28        87.22        97.84        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LR TCGA-B6-A0I1 
       79.00        89.00        93.83        54.21        20.38        77.62 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RG 
      129.57       112.37       176.98       110.14       211.56        68.45 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY 
      102.77       100.70       131.21        79.63        21.47       113.79 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40C 
       43.59       101.52        73.51        74.99        68.12        71.15 
TCGA-BH-A0AU TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       24.53        40.83        48.36        56.94        51.68        37.22 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       44.05        45.57        49.05        41.75        44.02        42.90 
TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0H7 
       15.65        47.41         4.41         9.63        24.49        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       41.00        13.61        12.89        27.25        50.79         5.59 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18T 
       44.81         8.81        20.12        90.84        26.66         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1F6 
       51.39        69.93        91.99       113.82        12.00        97.48 
TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12P 
      114.15        45.63        72.07        57.83        18.64        11.77 
TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HN 
       12.66         1.05         4.08        10.92        12.03         3.25 
TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 
        0.43         9.50        12.20        13.02        20.88        13.97 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       21.14        14.17        17.49        18.90        12.03        12.03 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XQ 
       18.15        15.22        21.83        19.92        15.55        16.41 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M 
       16.31        12.99        16.54        15.32         9.93        13.48 
TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14V 
       16.18        12.10        46.59        40.11        44.68        34.26 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15H 
       25.41        27.12        19.43        25.05        18.21        12.92 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 
       60.53        17.10        37.41        33.70        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       24.59         8.75        16.93        34.92        26.56        34.29 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1R4 
       13.48        13.12        36.56        39.55        12.59         6.12 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 
       40.24        34.65         6.58        21.27        34.59        34.13 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       41.03        12.89        23.51         0.69        27.22         1.94 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL 
        7.13         0.72        26.07        30.18        15.72         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       13.81        14.40        25.94        29.85        40.41        41.13 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
        7.86         6.15        19.96        55.00        52.73        25.91 
TCGA-EW-A3E8 TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A441 
       34.03        72.10        69.30         2.60        11.57        11.44 
TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A8F5 TCGA-OL-A5D7 
       14.70        14.79        22.26        16.08        14.73        58.52 
TCGA-OL-A66I TCGA-OL-A66K TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZF TCGA-S3-A6ZG 
       23.47        41.92        64.21        86.96        16.50        13.12 
TCGA-S3-AA10 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-WT-AB44 TCGA-Z7-A8R5 
       15.39        13.94        52.96        29.03       108.07 

$`15Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       47.24        13.68        31.79         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
      104.81       121.94        63.12        55.43        36.13       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV 
      114.81        92.48        88.60       107.93         5.19        98.99 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP 
       34.55        33.76        61.58        25.22       101.72       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       99.19        44.28        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       21.67        49.48        19.33        48.46        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        39.65        83.01        32.75        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       34.98        50.37        24.39        21.30        23.21        21.14 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       25.15        23.61        29.56        23.74        23.80        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        13.74        21.17        12.10        10.72        11.05 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        53.06        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       17.03         9.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       32.05         9.99        10.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        18.05        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        33.01        19.96        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 
       33.01       112.08        40.01        33.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
       33.07        25.02         8.98        19.04        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       38.04         0.95        10.85         5.72         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.92        32.45        16.31        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ 
       18.67        12.26         1.68         8.22         0.03         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        0.62         1.78         1.71         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         5.65         7.96         7.59         7.17         6.28 
TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J8 
       58.95        32.78        21.40        52.18        26.04        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      106.78        90.58        98.27        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L 
       28.37        14.73        82.62        70.39        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        5.65        15.62        32.52        19.20       111.32        73.64 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       74.79        98.93       107.24        83.87       114.02        85.97 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       37.81        76.21        61.28        62.14       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       94.22        96.89        78.51        84.20         2.76        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       53.36        83.77        78.48        73.18        72.76        58.92 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      143.21        20.25        62.86        66.15        52.11        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        54.74        16.04        20.45        10.59 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      146.50        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      140.48        89.46       157.41        97.48       188.68        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW 
      139.17       170.17        85.35       103.63        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 
       25.55        28.50        46.95        39.55        39.16        56.98 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       35.67        48.69        27.19        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       11.67        48.13        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       38.47        67.86        16.27        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        32.58        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB 
       15.16        37.78        35.51        24.56        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0W3 
       20.38         5.85         2.50        36.85        51.32        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18M 
       24.95        42.35        23.05         2.01         7.23        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V 
       37.74        30.28        55.63        37.55        66.05        51.16 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        89.16        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU 
      122.89        36.92        63.35        55.00       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        26.14        38.60        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28         8.94        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66         0.39         3.16         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        1.12         4.11        12.33        11.34        11.28         0.16 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       10.42         2.30         0.30         0.23         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         9.53         0.03         0.99         0.03         0.23 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        11.90        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       14.17        13.48        19.20        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       18.15        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XR 
       12.39        17.16        14.73        14.50        17.69        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
        6.35        15.16        12.66        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-E2-A105 
       12.26        33.37        18.51        21.67         8.02        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 
       43.33        32.02        31.96        28.60        18.51        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       20.71        21.63        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        32.78        33.73        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
       22.19        20.98        11.08        54.18        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90        18.87       106.75       102.61        43.04         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       15.72         8.28        30.61        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.82        12.00        35.77        35.24        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        28.27        34.95         2.56         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 
       21.21        32.09        32.09         1.12        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 
       12.53        13.32        39.09        22.75        20.71        17.06 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y 
       24.56        29.72         0.76        18.41        12.33        23.84 
TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.70        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW 
       18.90        13.25        16.57        15.68        28.77        22.82 
TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.95        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        18.90        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       34.55        22.09        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        62.43        11.84        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        7.10        13.28        10.62        24.95        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       17.06        15.32        14.47         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        14.70        12.36        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        16.93        16.80        13.84        15.35        14.96 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
       13.84        17.03         3.81        11.41        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.33               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            211.56             234.28 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             26.01              23.77 
[1] "0.3 - 211.6 (26.0)" "0.0 - 234.3 (23.8)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED        20       21        1        0       119        71
  15Q LOSS WILD-TYPE      69       60        7        3       234       174
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           1         49          5         16        6
  15Q LOSS WILD-TYPE         1        101         24         47       14
                    vv
clus                 STAGE TIS STAGE X
  15Q LOSS MUTATED           0       3
  15Q LOSS WILD-TYPE         1      10
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 21                 60
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA               119                234
  STAGE IIB                71                174
  STAGE III                 1                  1
  STAGE IIIA               49                101
  STAGE IIIB                5                 24
  STAGE IIIC               16                 47
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    61 209  34   9
  15Q LOSS WILD-TYPE 211 407  96  31
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               61                211
  T2              209                407
  T3               34                 96
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED   161  87  43  20
  15Q LOSS WILD-TYPE 340 263  74  55
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              161                340
  N1               87                263
  N2               43                 74
  N3               20                 55
[1] 4 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
  15Q LOSS MUTATED   268   6
  15Q LOSS WILD-TYPE 611  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    268    6
  15Q LOSS WILD-TYPE  611   15
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              268                611
  1                6                 15
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   311   3
  15Q LOSS WILD-TYPE 740   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    311    3
  15Q LOSS WILD-TYPE  740    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              311                740
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q LOSS MUTATED                            0                           249
  15Q LOSS WILD-TYPE                          1                           514
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q LOSS MUTATED                               33                   3
  15Q LOSS WILD-TYPE                            159                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q LOSS MUTATED                       2                               10
  15Q LOSS WILD-TYPE                     2                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  15Q LOSS MUTATED                    2             15
  15Q LOSS WILD-TYPE                 15             33
D68V8, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 249                514
  INFILTRATING LOBULAR CARCINOMA                 33                159
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 15                 33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    98 216
  15Q LOSS WILD-TYPE 190 558
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     98  216
  15Q LOSS WILD-TYPE  190  558
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                98                190
  YES              216                558
[1] 2 2
[1] FALSE
D68V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0    15
  15Q LOSS WILD-TYPE                                1    45
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          57   214
  15Q LOSS WILD-TYPE                       113   522
D68V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                 45
  BLACK OR AFRICAN AMERICAN                      57                113
  WHITE                                         214                522
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8 256
  15Q LOSS WILD-TYPE  30 602
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8  256
  15Q LOSS WILD-TYPE   30  602
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 30
  NOT HISPANIC OR LATINO              256                602
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   149  20
  16P LOSS WILD-TYPE 767 108
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               169                875 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                108 
$`16P LOSS MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CR 
       43.43        31.79        39.32        73.84        87.25       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0EY 
       75.25        98.99        67.33        25.22        79.76        63.29 
TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A1FX TCGA-A2-A3XT TCGA-A2-A4RY 
       50.43        20.75        32.55        60.72        83.01        21.30 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       38.30        34.29        35.47        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZW 
       25.15        23.61        20.61        14.50        14.73        10.72 
TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07L TCGA-A8-A08J 
        9.37        13.02        17.03        43.00        32.05        37.05 
TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09W TCGA-AC-A2BK 
       43.00        33.07         1.02        25.02         0.99        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP 
       99.35        40.57        55.43        13.58         0.03        20.19 
TCGA-AC-A8OQ TCGA-AN-A046 TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FN TCGA-AN-A0XN 
        1.12         0.33         6.51         0.33         7.17         0.33 
TCGA-AN-A0XR TCGA-AO-A0JD TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12G TCGA-AO-A1KT 
        0.33        72.00       108.03        98.27        41.62        17.79 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A1AR 
       32.52         2.56       114.02        75.55        43.07        17.23 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 
      160.90        50.89        84.20        53.36        85.35        78.48 
TCGA-AR-A2LR TCGA-B6-A0I5 TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL 
       20.38       149.59       176.98       211.56       189.01        81.17 
TCGA-B6-A0X0 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-BH-A0B4 TCGA-BH-A0B6 
      129.70        43.59       170.17        74.99        39.16        56.94 
TCGA-BH-A0BO TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0H5 
       35.67        41.75        31.17         4.41        14.30        35.51 
TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A1EN 
       13.61        51.32        50.79        90.84        51.39        69.93 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FL 
       82.85        42.28        55.69       114.15        33.17        55.00 
TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A5IZ TCGA-BH-A8FZ TCGA-BH-A8G0 
       38.60       130.16         6.44        18.64        18.87        21.76 
TCGA-C8-A130 TCGA-C8-A1HG TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        3.16        11.34         0.36         9.50         0.99         0.03 
TCGA-D8-A1JC TCGA-D8-A1JN TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A27V TCGA-D8-A3Z6 
       15.78        20.38        13.32        14.70        12.53        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 
       21.67        16.18        32.02        28.60        25.41        25.05 
TCGA-E2-A15J TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1II 
       19.40        17.06        14.07        14.99        60.53        33.70 
TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1ND 
        3.88        27.42         8.75        34.92        26.56        12.59 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-EW-A1J5 TCGA-EW-A1J6 
       41.03        23.51         0.69         1.94        15.68        28.77 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DC 
        7.86         6.15        17.49        10.16        59.57        83.34 
TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-HN-A2NL 
       72.10        85.35        38.20        69.30        72.03         2.60 
TCGA-HN-A2OB TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 
       62.43        25.05        14.70        12.36        14.73        58.52 
TCGA-OL-A5RW TCGA-OL-A66L TCGA-OL-A6VO TCGA-PE-A5DC TCGA-S3-AA0Z TCGA-S3-AA10 
       36.36        42.77        28.21        47.01        16.80        15.39 
TCGA-S3-AA12 
       15.35 

$`16P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       104.81        18.02        78.41       121.94        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        92.48        88.60        75.55         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       56.81        34.55        33.76        61.58       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       107.61        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        17.46        18.90        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        23.47        17.36        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        38.37         7.30        24.39        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        21.90        35.31        37.45        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       20.19        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY 
       17.92        12.10        11.05        10.29        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        12.00         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        45.07        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       33.01       112.08        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T 
       50.04        49.05        45.07        29.98         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       10.85         5.72         1.48        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70        33.04         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55        11.44        13.71        17.42        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
       12.26         1.68         8.22         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.36         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.96         7.00         7.59         6.28         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
       12.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.72       106.78        90.58        64.04        57.30        48.36 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O 
       24.79        26.93       130.09         5.65        15.62        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       111.32        73.64         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       42.35        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      101.95        83.87        85.97        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
       48.82        76.11        43.73        43.56        39.98        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       76.21        61.28        63.62        62.14        33.73        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       96.89        78.51         2.76       104.28        87.22        97.84 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       76.01        50.96        83.77        79.00        89.00        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      140.88        68.45       234.28        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.57       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       73.51       139.17        85.35        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       24.53        59.84        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       40.83        39.55        48.36        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        11.67        49.05        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       47.41        16.27        15.68         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU 
       26.50        20.38         5.85         2.50        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       23.05         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EX 
        7.36        51.16        91.99       113.82        12.00        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM 
      120.62        74.73       122.89        36.92        63.35        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 
       72.07       144.59        72.07        28.14        26.14        83.31 
TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       57.83        10.65        20.12        10.52       109.28         8.94 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-AB28 TCGA-C8-A12L 
       23.51         9.63         5.26         9.70         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         0.39         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.12         1.05         4.11         4.08        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.23         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        0.03        12.20         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        18.71        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69        15.55 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       13.08        12.26        33.37         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        34.26        31.96 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        17.42         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       13.02        19.56        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.73        28.44        22.65        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.87       106.75       102.61        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       15.72         8.28        30.61        34.29        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       32.88        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       39.55        35.77        35.24        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        32.09        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       17.06        27.22         7.13        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        18.90        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB 
       34.03        23.51         7.40       109.87       216.76        79.10 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX 
      101.62       110.50        43.73        66.38        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YL TCGA-LL-A5YM 
       10.62        24.95        11.44        10.95        17.06        15.32 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        14.70        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       28.87        24.72        22.32        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        41.92        26.04        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11         8.91        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 
        9.93        16.50        13.12        16.93        13.84        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            211.56             234.28 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             32.02              23.47 
[1] "0.0 - 211.6 (32.0)" "0.0 - 234.3 (23.5)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED        20       10        1        0        68        33
  16P LOSS WILD-TYPE      69       71        7        3       285       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         21          5         11        1
  16P LOSS WILD-TYPE         2        129         24         52       19
                    vv
clus                 STAGE TIS STAGE X
  16P LOSS MUTATED           0       1
  16P LOSS WILD-TYPE         1      12
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 10                 71
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                68                285
  STAGE IIB                33                212
  STAGE III                 0                  2
  STAGE IIIA               21                129
  STAGE IIIB                5                 24
  STAGE IIIC               11                 52
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    43 100  20   7
  16P LOSS WILD-TYPE 229 516 110  33
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               43                229
  T2              100                516
  T3               20                110
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    95  45  17  13
  16P LOSS WILD-TYPE 406 305 100  62
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               95                406
  N1               45                305
  N2               17                100
  N3               13                 62
[1] 4 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
  16P LOSS MUTATED   148   1
  16P LOSS WILD-TYPE 731  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    148    1
  16P LOSS WILD-TYPE  731   20
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              148                731
  1                1                 20
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   169   2
  16P LOSS WILD-TYPE 882   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    169    2
  16P LOSS WILD-TYPE  882    9
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE              169                882
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P LOSS MUTATED                            0                           132
  16P LOSS WILD-TYPE                          1                           631
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P LOSS MUTATED                               26                   3
  16P LOSS WILD-TYPE                            166                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P LOSS MUTATED                       1                                3
  16P LOSS WILD-TYPE                     3                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16P LOSS MUTATED                    0              6
  16P LOSS WILD-TYPE                 17             42
D69V8, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 132                631
  INFILTRATING LOBULAR CARCINOMA                 26                166
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  6                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    41 130
  16P LOSS WILD-TYPE 247 644
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     41  130
  16P LOSS WILD-TYPE  247  644
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                41                247
  YES              130                644
[1] 2 2
[1] FALSE
D69V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    11
  16P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          42   106
  16P LOSS WILD-TYPE                       128   630
D69V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 49
  BLACK OR AFRICAN AMERICAN                      42                128
  WHITE                                         106                630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7 141
  16P LOSS WILD-TYPE  31 717
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7  141
  16P LOSS WILD-TYPE   31  717
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 31
  NOT HISPANIC OR LATINO              141                717
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   508  62
  16Q LOSS WILD-TYPE 408  66
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               570                474 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                62                 66 
$`16Q LOSS MUTATED`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SE 
       40.14        11.44        48.56        48.36        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       48.10        47.24        31.79         7.96        39.32        28.01 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A0CK 
      104.81       121.94        73.84        87.25        63.12       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       98.99        67.33        34.55        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY 
      134.40        80.28        79.76        34.29        24.72        63.29 
TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       54.64        44.28        17.13        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       20.75        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 
       19.33        48.46        31.73        23.47        60.72        20.25 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A4RY 
       52.47       107.70        20.88        39.65        83.01        21.30 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB 
       21.90        38.30        34.29        35.47        30.61        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26I 
       31.73        25.15        23.61        29.56        31.36        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB 
       20.61        22.32        10.59        11.28        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        21.17        14.73        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X 
        9.37        13.02        13.02         1.02        29.03        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07J 
       17.03         9.01        43.00        19.99        18.97        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A086 
       32.05        10.98         8.98         7.99        15.06        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
        0.99        38.01        28.96        19.96        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09K 
       30.97        17.95        41.98         9.99        12.00        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04         2.37        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FM 
       38.53        99.35        40.57        55.43        36.99        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
       50.70         0.92        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX 
       16.57        19.79         1.55        13.71        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS 
        1.68         8.22         0.03        20.19         1.12         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FK 
        0.33         0.33         0.33         7.36         0.33         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        7.17         6.28         0.33         0.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         0.33        80.28        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       95.70        68.75        21.40        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 
       21.53        72.00        21.37        50.24        62.04        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G 
      108.72       108.03        90.58        98.27        57.30        41.62 
TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       82.62         0.53        17.79        15.62        32.52         2.56 
TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AK 
       42.35       107.24        83.87       114.02        75.55        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       48.82        76.11        43.73        39.98        43.07        17.23 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        50.89        94.22        78.51        84.20         2.76 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A251 
       97.84        76.01        53.36        85.35        83.77        78.48 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       72.76       143.21        62.86        54.21        66.15        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       38.17        39.39        16.04       149.59       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       50.70       112.37       126.12       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RP 
       68.45       189.01       234.28        81.17       172.96       102.77 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X7 
      157.41        97.48        18.35       129.57       129.70        58.88 
TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       43.59       170.17        74.99        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       24.53        59.84        25.55        46.95        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BM 
       48.36        56.94        56.98        37.22        25.71        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C1 
       35.67        48.69        27.19        53.95        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO 
       48.13        42.90        31.17        38.01        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 
       15.65         2.56        38.47        67.86        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        30.35        15.16        37.78        35.51 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W7 
       51.32        27.25        50.79        23.93        24.95        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P 
       23.05         8.81        20.12        90.84        37.74        30.28 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
        7.36        51.39        69.93        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FC 
       12.00        55.69        17.69        31.53        89.16       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A202 TCGA-BH-A203 
       33.17        74.73       122.89        55.00        26.14        38.60 
TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42V TCGA-BH-A5IZ 
      130.16         6.44        20.12        10.52         8.94        18.64 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12Z 
        9.70        18.87        21.76         9.44        11.77         0.39 
TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        3.16         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A274 
       11.28         2.30         3.25         0.23         0.36         9.53 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z 
        9.50         0.99         0.03        12.49        11.90        20.88 
TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        14.17        17.49        15.78        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       12.03        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1XK 
       13.32        14.70        18.58        17.79        25.74        14.50 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.55        16.41        15.85        16.31        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P 
        9.93        14.14        13.45         9.44        16.41         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.53        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
        8.02        12.10        34.42        40.41        40.11        28.44 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       44.68        38.24        33.17        43.33        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       18.51        25.41        23.24        21.04        23.87        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S 
       19.40         9.04        20.58        13.02        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       14.99        60.53        33.01        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 
       37.41        33.73        33.70         3.88        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A2P5 
       27.42        39.62        24.59        18.87         8.75        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        26.56        34.29 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG 
       32.88        36.82        12.00        12.59        35.24        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        28.27         2.56         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
       21.21        32.09        32.09         1.12        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       35.64        34.13        32.05        41.03        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.71         0.69         1.94         7.13        24.56         0.72 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.07        15.72        23.84        14.40        15.39        12.20 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PC 
       25.94        40.41        52.96        18.48         7.86         6.15 
TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       10.52        34.55        52.73        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI 
       23.51         7.40        59.57        83.34        72.10        85.15 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 
      101.62        85.35       110.50        38.20        69.30        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12         2.60        62.43        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FP 
       13.22        13.28        25.05        17.06        14.70        22.26 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 
       12.36        14.73        27.91        22.39        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 
       31.99        58.62        34.92        36.36        28.87        20.38 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ 
       65.62        41.92        42.77        26.04        28.21        19.73 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       47.01        64.21        16.50        13.12        16.80        15.39 
TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        11.41        29.03        15.35        16.04       107.05 

$`16Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG 
      129.14       131.67        42.81         9.96         8.52        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       20.88        13.68        19.20        18.21        18.02        78.41 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CU 
      101.98        55.43        36.13        99.12        24.79         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      107.93        56.81        33.76       107.61        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        31.82        61.94        99.19        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YI 
       50.43        17.52         8.38        49.84        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 
       18.61        23.77        17.36        22.45        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        38.37         7.30        24.39        23.21        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13E 
       21.14        35.31        37.45        35.67        29.79        20.19 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF 
       24.26        23.74        23.80        11.34        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VX TCGA-A7-A6VY 
       14.70        11.97        17.92        12.10        10.42         8.75 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07G 
       17.98        53.06        26.01         1.02        53.98        18.97 
TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       14.01         9.99        24.99         9.99        45.07        18.05 
TCGA-A8-A085 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A097 
       36.95        33.01        12.00         9.99         0.99        12.00 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A0A7 
        9.99         1.02        50.04        49.05        45.07         0.99 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3BB 
        0.95         5.72        38.79        33.04         2.27        32.45 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OR 
       23.24        24.79        11.44        17.42        18.67         1.32 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.59         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33        12.33         5.33         5.59        61.35 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        32.78        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL 
       37.48        50.70        50.86        76.77        26.24        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12H 
       71.80       102.58       106.78        64.04        48.36        28.37 
TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       14.73        61.87        70.39        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        5.65        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       74.79        86.66        98.93        64.83        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AS 
      101.95        85.97        61.84        52.77        43.56        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M 
       76.21        61.28        63.62        62.14        33.73        96.89 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
      104.28        87.22        50.96        79.00        89.00        73.18 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       58.92        93.83        20.25        40.54        20.38        54.74 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IE 
       20.45        10.59        77.62       143.38        12.13        65.72 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RM 
      146.50       176.98        18.77        84.59       110.14        78.02 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WT 
      162.05       140.48       100.70        89.46       131.21       188.68 
TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       79.63        21.47       113.79       186.48        28.27        68.94 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-BH-A0AW TCGA-BH-A0AZ 
      101.52        73.51       139.17        85.35        20.45        28.50 
TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ 
       39.55        51.68        32.02        18.21        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       44.05        53.69        45.57        49.94        11.67        49.05 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DX 
       45.83        23.44        22.13        48.23         3.22        47.41 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       24.43        10.78        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18L 
       26.50         5.59        42.35         2.01         7.23        26.66 
TCGA-BH-A18M TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ES 
       72.56        55.63        37.55        66.05        51.16       113.82 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FH 
       49.58        25.81        97.48        24.66       120.62        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A5J0 TCGA-BH-A6R8 
       83.31        57.83        10.65       109.28        23.51         9.63 
TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        5.26        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66        12.66         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V 
        1.12         1.05         0.16        12.03        10.42         0.30 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 
        0.43         8.28         9.67         0.03        12.20         0.23 
TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 
       13.02        13.41        19.46        13.25        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF 
       13.48        21.14        19.20        16.50        18.71        12.03 
TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1X7 TCGA-D8-A1X9 
       14.01        20.12        20.09        19.40        16.73        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       21.83        19.92        17.69         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H 
       12.66        15.32        14.24        17.42        16.04        13.05 
TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 
       14.43        13.48         4.80        10.09        12.26        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       27.52        46.59        37.51        28.87        47.15        40.96 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 
       38.60        33.30        34.26        31.96        27.12        19.43 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 
       14.79        23.34        21.63        11.05        19.56        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       53.03        32.35        28.50        32.78        28.44        22.65 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       22.19        20.98        19.66        40.47        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N6 
      102.61        43.04         8.28        12.85        34.82        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1R2 
       13.12        36.56        39.55        35.77         9.86        34.95 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       40.24         6.58        34.59        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
       22.75        17.06        27.22        29.72         0.76        18.41 
TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX 
       30.18        12.33        14.70         0.79        13.81        39.72 
TCGA-EW-A1J1 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       18.90        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       29.82        23.11        30.08        18.90        19.99        13.94 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C9 
       14.43        19.96        55.00        25.91        22.09       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        79.10        75.02        70.85        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A3XG TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF 
      106.06        43.73        66.38        11.84         7.10        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       24.95        11.44        10.95        15.32        14.47        14.79 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        14.70 
TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       14.07         2.10        40.08        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE 
       23.47        17.36        14.07        40.11         8.91        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 
        0.16         0.26         9.93        16.93        13.84        14.96 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB41 TCGA-Z7-A8R5 
       13.84        13.94        17.03         3.81        52.96       108.07 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            234.28             216.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            24.985             23.850 
[1] "0.0 - 234.3 (25.0)" "0.0 - 216.8 (23.9)"
[1] "hr=" "1.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        55       42        4        2       203       128
  16Q LOSS WILD-TYPE      34       39        4        1       150       117
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         80         13         35        7
  16Q LOSS WILD-TYPE         1         70         16         28       13
                    vv
clus                 STAGE TIS STAGE X
  16Q LOSS MUTATED           0       8
  16Q LOSS WILD-TYPE         1       5
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  55                 34
  STAGE IA                 42                 39
  STAGE IB                  4                  4
  STAGE II                  2                  1
  STAGE IIA               203                150
  STAGE IIB               128                117
  STAGE III                 1                  1
  STAGE IIIA               80                 70
  STAGE IIIB               13                 16
  STAGE IIIC               35                 28
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   8                  5
[1] 13  2
[1] TRUE
[1] "dimension of 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   152 334  75  18
  16Q LOSS WILD-TYPE 120 282  55  22
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1              152                120
  T2              334                282
  T3               75                 55
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q LOSS MUTATED   290 179  60  44
  16Q LOSS WILD-TYPE 211 171  57  31
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              290                211
  N1              179                171
  N2               60                 57
  N3               44                 31
[1] 4 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
  16Q LOSS MUTATED   480   8
  16Q LOSS WILD-TYPE 399  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    480    8
  16Q LOSS WILD-TYPE  399   13
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              480                399
  1                8                 13
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   576   4
  16Q LOSS WILD-TYPE 475   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    576    4
  16Q LOSS WILD-TYPE  475    7
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE              576                475
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q LOSS MUTATED                            0                           387
  16Q LOSS WILD-TYPE                          1                           376
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q LOSS MUTATED                              150                   3
  16Q LOSS WILD-TYPE                             42                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q LOSS MUTATED                       1                               18
  16Q LOSS WILD-TYPE                     3                               12
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16Q LOSS MUTATED                    3             17
  16Q LOSS WILD-TYPE                 14             31
D70V8, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 387                376
  INFILTRATING LOBULAR CARCINOMA                150                 42
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 12
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                 17                 31
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   148 432
  16Q LOSS WILD-TYPE 140 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    148  432
  16Q LOSS WILD-TYPE  140  342
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               148                140
  YES              432                342
[1] 2 2
[1] FALSE
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1    29
  16Q LOSS WILD-TYPE                                0    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          85   403
  16Q LOSS WILD-TYPE                        85   333
D70V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          29                 31
  BLACK OR AFRICAN AMERICAN                      85                 85
  WHITE                                         403                333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    20 454
  16Q LOSS WILD-TYPE  18 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     20  454
  16Q LOSS WILD-TYPE   18  404
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   20                 18
  NOT HISPANIC OR LATINO              454                404
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   484  75
  17P LOSS WILD-TYPE 432  53
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               559                485 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                75                 53 
$`17P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
       14.37        43.43        48.10        47.24        20.88        31.79 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R 
       39.32        28.01        19.20        18.21        18.02       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        87.25        63.12       101.98        36.13       136.73 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79       114.81       107.93        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO 
      107.93        67.33        34.55        25.22       134.40        80.28 
TCGA-A2-A0EQ TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       79.76        24.72        63.29        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC 
       44.28        17.13        49.84        20.52        20.75        32.55 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       18.21        21.90        21.67        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A2-A25B 
       17.36        20.25        19.20        19.56       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       18.15        39.65        83.01        32.75        49.48        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG 
       38.37         7.30        24.39        26.96        21.90        34.29 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H 
       30.61        37.45        35.67        31.73        25.15        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       31.36        24.26        23.74        23.80        21.73        22.32 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q 
       11.05         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        29.03        31.00         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L 
        9.01        43.00        19.99        18.97        14.01        32.05 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B 
        8.98         9.99        15.06        36.95        13.02        38.01 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 
       33.01         9.99        31.00         0.99        43.00        30.97 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       17.95         9.99         1.02        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 
        1.02         8.98        14.01        19.04        13.02         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       17.03        38.04         0.95         2.37        38.53        99.35 
TCGA-AC-A2FB TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3TN 
       40.57         0.92         2.27        32.45        14.83        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A7VB TCGA-AC-A8OS 
       16.57        19.79        13.71        17.42         8.22         2.30 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL 
        0.23         0.33         1.78         1.71         9.96         6.51 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.16         0.33         0.33         6.44         7.96         7.59 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.59        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        29.13        32.78        21.40        52.18 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A0JM 
       21.53        50.70        72.00        76.77        62.04        71.80 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KS 
      108.72       108.03        64.04        41.62        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09         5.65        32.52         2.56 
TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY 
       32.91       111.32         5.26        86.66        98.93        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       101.95        83.87       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR 
       61.84        52.77        76.11        43.73        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       37.81        76.21        62.14        33.73       160.90        94.22 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       84.20         2.76        97.84        76.01        53.36        85.35 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       79.00        89.00        72.76        58.92        93.83       143.21 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE 
       62.86        52.11        54.74        12.13       129.57        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WY 
      100.70       131.21       157.41        97.48        79.63       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AV 
      129.57        58.88       139.17        74.99        68.12        59.84 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       25.55        46.95        40.83        48.36        56.94        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ 
       37.22        32.02        25.71        61.68        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE 
       53.69        11.67        49.05        44.02        45.83        31.17 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0DZ 
       22.13        13.91        48.23        15.65        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI 
        4.41        14.30         9.63        46.19        31.00        24.43 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HP 
       15.16        23.08        52.96        26.50         5.85        13.61 
TCGA-BH-A0HU TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       12.89        24.95        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T 
       20.12        26.66        30.28        55.63        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU 
       51.39        51.16        69.93        91.99       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FE 
       12.00        17.69        97.48        24.66        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A201 
      122.89        36.92        63.35        45.63        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ 
       26.14        38.60        57.83       130.16        10.52        18.64 
TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
       23.51        18.87        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         0.39         2.24         1.12         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11         4.08        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         2.30         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP 
        8.28         9.50        12.20         0.99         0.03        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A146 
       12.49        19.46        11.90        20.88        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD 
       19.20        14.17        17.49        16.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.90        12.03        20.12        19.40        20.38        21.01 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XF 
       13.32        18.58        16.73        23.90        27.58        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XT 
       21.83        14.50        19.92        17.69        16.41         6.35 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27R 
       14.14        13.45        13.05        13.48         4.80        10.09 
TCGA-D8-A27T TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A10C TCGA-E2-A10F 
       13.08        16.18         8.02        43.00        40.11        28.87 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y 
       38.24        38.60        33.17        34.26        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 
       18.51        25.41        27.12        23.24        21.04        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       25.05        23.34        20.71        18.21        12.92        17.42 
TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1IE TCGA-E2-A1IG 
       11.05        14.07        14.99        60.53        38.30        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 
       33.73        33.70        28.44        20.98        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       24.59        28.90        18.87        43.04        16.93         5.52 
TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 
        8.28        34.92        34.29        12.85        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       12.00        13.12        36.56        39.55        12.59        35.24 
TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF 
        6.12        21.21        32.09        32.09        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B 
       21.27        35.64        34.13        12.53        39.09        22.75 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       41.03        23.51         0.69        27.22         0.72        29.72 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO 
       26.07        30.18        15.72        12.33         0.79        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       14.40        15.39        12.20        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 
       15.68        28.77        25.94        40.41        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       23.11         7.86        18.90        13.94        10.52        14.43 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       55.00        25.91        34.03         7.40       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       79.10        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF 
      115.69        69.30        11.84        13.22         7.10        10.62 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 
       15.32        14.70        14.47         7.46        14.50        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.73        14.07        27.91        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DC 
       58.62        36.36        22.32        20.38        23.47        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA17 
       64.21        86.96        16.50        16.93        15.39        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A89A 
       17.03         3.81        11.41        52.96        29.03        16.04 
TCGA-Z7-A8R6 
      107.05 

$`17P LOSS WILD-TYPE`
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.36         9.96         8.52        14.27        13.68         7.96 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ 
      104.81        78.41        55.43        99.12        92.48        88.60 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP 
       75.55        56.81        33.76        61.58       101.72       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 
       99.19        54.64        17.52         8.38        17.46        18.90 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT 
       25.28        50.47        49.48        18.61        31.73        23.77 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E 
       60.72        22.45        16.47        52.47        17.19       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ 
       10.59        20.88        33.93        29.98        47.31        50.37 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH 
       21.30        23.21        21.14        38.30        35.31        35.47 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A3IY 
       33.11        29.79        20.19        23.61        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Y 
       12.10        10.72        10.29        13.02        53.06        26.01 
TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        12.00         9.99        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
       45.07        18.05         0.99        28.96        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       37.05        31.00        33.01       112.08        40.01        33.01 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       41.98        12.00         9.99        12.00        50.04        49.05 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 
       25.02        19.04        15.02         0.99        12.00        21.04 
TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG 
       27.02        10.85         5.72         1.48        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QP 
       38.79        26.04        50.70        33.04        16.31        22.19 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79         1.55        11.44        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
       12.26         1.68         0.03        20.19         1.12         1.32 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AR 
        0.33         0.33         0.62         2.96         7.36         0.33 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XS TCGA-AN-A0XV 
        5.65         7.00         7.17         6.28         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       80.28        58.95        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JL 
       53.03        50.86        21.37        26.24        50.24        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
      102.58        99.25       106.78        90.58        98.27        57.30 
TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       48.36        28.37        14.73        82.62        61.87        17.79 
TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX 
       15.62        19.20        73.64        74.79        42.35        64.83 
TCGA-AR-A0U0 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AV 
       65.36        51.25        48.82        43.56        39.98        61.28 
TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24R 
       63.62        50.89        96.89        78.51       104.28        87.22 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LK 
       50.96        83.77        78.48        73.18        20.25        54.21 
TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       66.15        38.17        39.39        40.54        20.38        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       50.70       110.93        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      102.77       140.48        89.46       188.68        18.35        21.47 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       73.51       170.17        85.35       103.63        71.15        24.53 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD 
       20.45        28.50        39.55        39.16        56.98        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BS TCGA-BH-A0BT 
       24.85        21.70        44.05        35.67        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH 
       49.94        41.75        48.13        42.90        23.44        38.01 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E1 
       17.26         3.22         2.56        38.47        67.86        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       44.81        32.58        24.49        30.35        10.78        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HQ 
       35.51        24.56        41.00        20.38         2.50        36.85 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W5 
       51.32        27.25        50.79         5.59        23.93        42.35 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ET 
       44.81        90.84        72.56        37.74        37.55        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       55.69        49.58        25.81        31.53        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A28O 
      114.15        55.00       144.59        72.07        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 
        6.44        20.12       109.28         8.94         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A12W 
        9.70        21.76         9.44        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HN 
       12.66         3.16         1.87        12.33        11.28         3.25 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A140 
        9.67         9.53         0.03         0.23        13.41        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH 
       20.58        13.97        14.17        18.71        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 
       18.97        20.09        20.09        12.20        14.70        17.79 
TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO 
       25.74        18.15        12.39        17.16        14.73        15.55 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A27E TCGA-D8-A27F 
       15.85        16.31        15.16        12.66        17.42        16.04 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W 
       14.43         9.44        16.41         0.76        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 
       33.37        18.51        21.67        12.10        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O 
       46.59        40.41        37.51        28.44        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A156 
       40.96        33.30        43.33        32.02        19.43        23.87 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       22.82        17.29        21.63        19.40         9.04        20.58 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       13.02        19.56        17.06        53.62        53.03        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IK 
       32.35        28.50        16.47        17.10        37.41        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
        3.88        22.19        11.08        54.18        19.66        40.47 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 
      106.75       102.61         8.75        15.72        30.61        26.56 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       34.82        32.88        35.77        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC 
       28.27        34.95         2.56         3.02         2.76        40.24 
TCGA-E9-A1RD TCGA-E9-A1RH TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A22H 
        1.12        34.59        32.05        13.32        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 
       17.06         1.94         7.13        24.56         0.76        18.41 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1OW 
       23.84        14.70        39.72         8.48        18.21        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        29.85        41.13        39.78        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW 
       19.99         6.15        34.55        19.96        52.73        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DK TCGA-GM-A2DM 
       17.49        10.16        23.51        59.57        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX 
       72.03        13.55        18.12         2.60        62.43        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24        13.28        24.95        11.44        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       14.70        22.39         2.10        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       24.72        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 
        0.16         0.26         9.93        13.12        16.80        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A899 TCGA-Z7-A8R5 
       15.35        14.96        13.84        15.35       108.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            234.28             220.90 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             24.39              24.56 
[1] "0.0 - 234.3 (24.4)" "0.0 - 220.9 (24.6)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED        43       39        2        2       185       141
  17P LOSS WILD-TYPE      46       42        6        1       168       104
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         85         11         37       11
  17P LOSS WILD-TYPE         2         65         18         26        9
                    vv
clus                 STAGE TIS STAGE X
  17P LOSS MUTATED           1       8
  17P LOSS WILD-TYPE         0       5
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  43                 46
  STAGE IA                 39                 42
  STAGE IB                  2                  6
  STAGE II                  2                  1
  STAGE IIA               185                168
  STAGE IIB               141                104
  STAGE III                 0                  2
  STAGE IIIA               85                 65
  STAGE IIIB               11                 18
  STAGE IIIC               37                 26
  STAGE IV                 11                  9
  STAGE TIS                 1                  0
  STAGE X                   8                  5
[1] 13  2
[1] TRUE
[1] "dimension of 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   124 353  72  17
  17P LOSS WILD-TYPE 148 263  58  23
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1              124                148
  T2              353                263
  T3               72                 58
  T4               17                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED   268 181  66  42
  17P LOSS WILD-TYPE 233 169  51  33
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              268                233
  N1              181                169
  N2               66                 51
  N3               42                 33
[1] 4 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
  17P LOSS MUTATED   476  12
  17P LOSS WILD-TYPE 403   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    476   12
  17P LOSS WILD-TYPE  403    9
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              476                403
  1               12                  9
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   565   4
  17P LOSS WILD-TYPE 486   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    565    4
  17P LOSS WILD-TYPE  486    7
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              565                486
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P LOSS MUTATED                            0                           428
  17P LOSS WILD-TYPE                          1                           335
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P LOSS MUTATED                               88                   5
  17P LOSS WILD-TYPE                            104                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P LOSS MUTATED                       2                               18
  17P LOSS WILD-TYPE                     2                               12
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17P LOSS MUTATED                    6             21
  17P LOSS WILD-TYPE                 11             27
D71V8, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 428                335
  INFILTRATING LOBULAR CARCINOMA                 88                104
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 12
  MUCINOUS CARCINOMA                              6                 11
  OTHER  SPECIFY                                 21                 27
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   152 417
  17P LOSS WILD-TYPE 136 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    152  417
  17P LOSS WILD-TYPE  136  357
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               152                136
  YES              417                357
[1] 2 2
[1] FALSE
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1    39
  17P LOSS WILD-TYPE                                0    21
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          97   383
  17P LOSS WILD-TYPE                        73   353
D71V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          39                 21
  BLACK OR AFRICAN AMERICAN                      97                 73
  WHITE                                         383                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    20 467
  17P LOSS WILD-TYPE  18 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20  467
  17P LOSS WILD-TYPE   18  391
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   20                 18
  NOT HISPANIC OR LATINO              467                391
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   233  33
  17Q LOSS WILD-TYPE 683  95
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               266                778 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                33                 95 
$`17Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       42.81        40.14        31.79        39.32        28.01        19.20 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CR 
       18.02        73.84        87.25       136.73        24.79       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0EN TCGA-A2-A0SW 
       75.25        98.99        67.33        34.55       134.40        44.88 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YK TCGA-A2-A1FW 
       50.43        17.13        32.55        18.21        19.33        17.36 
TCGA-A2-A1G1 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       19.20       107.70        42.44        83.01        32.75        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ 
       38.37        24.39        26.96        21.90        34.29        30.61 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       37.45        31.73        31.36        24.26        23.74        21.73 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW 
       13.74        14.50        21.17        14.73        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A076 
       10.42         8.75         1.02        17.98        31.00        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07R 
        9.01        43.00        19.99        14.01        32.05         8.98 
TCGA-A8-A084 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08X TCGA-A8-A093 
       15.06        13.02        38.01        12.00        43.00        17.95 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2BM 
       29.98         1.02         0.99        17.03        38.53        99.35 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62Y TCGA-AC-A8OS 
        2.27        32.45        16.57        19.79        17.42         2.30 
TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         1.78         6.51         0.33         7.96         7.59 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XR 
        7.04         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
        0.33         0.33        66.77        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A1KR 
       52.18        72.00        55.33       108.03        64.04        70.39 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TY TCGA-AR-A0U1 
        0.53         5.65         2.56       111.32        55.86       101.95 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AQ 
      114.02        75.55        61.84        52.77        43.73        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A250 TCGA-B6-A0IB 
       17.23        33.73        97.84        53.36        89.00       129.57 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      112.37       176.98       110.14       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 
      189.01       100.70       131.21       113.79       139.17        68.12 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       59.84        25.55        46.95        48.36        56.94        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0C1 
       37.22        32.02        48.69        53.69        11.67        44.02 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0H7 
        4.41        14.30         9.63        46.19        31.00        23.08 
TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       26.50        13.61        12.89         8.81         2.01         7.23 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU 
       30.28        55.63        51.16        69.93       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FM 
       12.00        17.69        97.48        33.17        36.92        45.63 
TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O 
       72.07        57.83        23.51        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A137 
       11.77        12.66        12.66         0.39         2.24         4.11 
TCGA-C8-A1HK TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27B 
       12.03         0.23         0.36         8.28         9.50         0.99 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A145 
        0.03        13.02        19.46        11.90        20.88        13.48 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JK 
       19.20        14.17        17.49        16.50        15.78        20.12 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT 
       19.40        20.38        21.83        14.50        16.41         6.35 
TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A73U TCGA-E2-A105 TCGA-E2-A14V 
       12.99        15.32        13.48        16.18        43.00        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        28.60        18.51        25.41        27.12        23.24 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II 
       14.79        25.05        18.21        11.05        60.53        33.70 
TCGA-E2-A1L7 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N6 
       27.42        43.04        16.93        34.92        34.29        13.48 
TCGA-E9-A1RA TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A295 
       32.09         6.58        21.27        41.03         0.69         0.72 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ 
       30.18        15.72         0.79        28.77        25.94        40.41 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       29.82         7.86        25.91         7.40       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 
       79.10        75.02        85.15        11.84        13.22         7.10 
TCGA-LD-A9QF TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW 
       10.62        14.70        14.47         7.46        58.52        36.36 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DD TCGA-PE-A5DE TCGA-UL-AAZ6 TCGA-UU-A93S 
       20.38        23.47        64.21        86.96        17.03         3.81 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`17Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       20.88        13.68         7.96        18.21       104.81        78.41 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL 
      121.94        63.12       101.98        55.43        36.13        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        92.48        88.60        75.55         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       56.81        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.28        17.52         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        20.75        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        18.61        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ 
       39.65        33.93        29.98        49.48        47.31        50.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
        7.30        21.30        23.21        21.14        38.30        35.31 
TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F 
       35.47        35.67        33.11        29.79        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        29.56        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O 
       14.93        17.92        12.10        10.72        11.05        13.02 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       18.97        18.97        12.00         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08A 
       24.99         9.99        45.07        18.05        36.95         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        33.01       112.08        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q 
        1.02        50.04        49.05        45.07        33.07        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        27.02        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        2.37        10.85         5.72         1.48        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ 
       16.31        14.83        22.19        14.99        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55        11.44        13.71        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.33         0.23         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.36         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FZ TCGA-AN-A0XL 
        5.65         7.00         7.17         6.28         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33        12.33         0.30         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       58.95        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      106.78        90.58        98.27        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52        32.91        19.20 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       73.64         5.26        74.79        86.66        42.35        98.93 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AK 
       64.83       107.24        65.36        83.87        85.97        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       48.82        76.11        43.56        39.98        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       61.28        63.62        62.14       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         2.76       104.28        87.22 
TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       76.01        85.35        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       220.90        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       65.72       146.50        18.77       126.12        84.59       110.93 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        74.99       103.63        71.15        24.53        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD 
       28.50        40.83        39.55        39.16        56.98        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.95        45.57        49.94        49.05        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        67.86        47.41        16.27        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        32.58        24.49        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX 
       20.38         5.85         2.50        36.85        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       23.05        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55        66.05         7.36        51.39        91.99        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       55.69        49.58        25.81        31.53        89.16        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62       114.15        74.73       122.89        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
        8.94        18.64         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       21.76         9.44        11.77        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
        3.16         1.87         1.12         1.05         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.28         0.16        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        3.25         0.30         0.43         9.67         9.53         0.03 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 
       12.20         0.23        12.49        13.41        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       13.97        14.17        21.14        18.71        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL 
       12.03        12.03        14.01        18.97        20.09        20.09 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        19.92        17.69        15.55 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.85        16.31        15.16        12.66        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       21.67         8.02        12.10        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       43.33        32.02        19.43        21.04        23.87        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       28.90        18.87       106.75       102.61         8.75         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 
       15.72         8.28        30.61        26.56        12.85        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        35.24        25.84         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH 
       21.21        32.09        40.24         1.12        34.65        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       22.75        12.89        23.51        20.71        17.06        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56        29.72         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       18.41        12.33        23.84        14.70        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        22.82        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF 
       17.49        10.16        23.51        59.57        83.34        70.85 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12         2.60        62.43        11.57        21.24 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        24.95        11.44        10.95        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       15.32        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J 
       34.92        28.87        24.72        22.32        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        9.93        16.50        13.12        16.93        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
       13.84        15.35        14.96        13.84        13.94        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        15.35       108.07       107.05 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.03               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            216.76             234.28 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            24.325             24.560 
[1] "0.0 - 216.8 (24.3)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED        19       23        1        0        94        59
  17Q LOSS WILD-TYPE      70       58        7        3       259       186
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         40          6         16        6
  17Q LOSS WILD-TYPE         2        110         23         47       14
                    vv
clus                 STAGE TIS STAGE X
  17Q LOSS MUTATED           0       2
  17Q LOSS WILD-TYPE         1      11
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 23                 58
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                94                259
  STAGE IIB                59                186
  STAGE III                 0                  2
  STAGE IIIA               40                110
  STAGE IIIB                6                 23
  STAGE IIIC               16                 47
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    62 162  34  11
  17Q LOSS WILD-TYPE 210 454  96  29
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               62                210
  T2              162                454
  T3               34                 96
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED   139  74  34  20
  17Q LOSS WILD-TYPE 362 276  83  55
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0              139                362
  N1               74                276
  N2               34                 83
  N3               20                 55
[1] 4 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
  17Q LOSS MUTATED   233   6
  17Q LOSS WILD-TYPE 646  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    233    6
  17Q LOSS WILD-TYPE  646   15
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0              233                646
  1                6                 15
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   270   0
  17Q LOSS WILD-TYPE 781  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    270    0
  17Q LOSS WILD-TYPE  781   11
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE              270                781
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q LOSS MUTATED                            0                           216
  17Q LOSS WILD-TYPE                          1                           547
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q LOSS MUTATED                               34                   3
  17Q LOSS WILD-TYPE                            158                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q LOSS MUTATED                       2                                5
  17Q LOSS WILD-TYPE                     2                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17Q LOSS MUTATED                    0             10
  17Q LOSS WILD-TYPE                 17             38
D72V8, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 216                547
  INFILTRATING LOBULAR CARCINOMA                 34                158
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                 10                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    74 196
  17Q LOSS WILD-TYPE 214 578
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     74  196
  17Q LOSS WILD-TYPE  214  578
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                74                214
  YES              196                578
[1] 2 2
[1] FALSE
D72V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    22
  17Q LOSS WILD-TYPE                                0    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          54   169
  17Q LOSS WILD-TYPE                       116   567
D72V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      54                116
  WHITE                                         169                567
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     9 216
  17Q LOSS WILD-TYPE  29 642
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9  216
  17Q LOSS WILD-TYPE   29  642
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 29
  NOT HISPANIC OR LATINO              216                642
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   253  53
  18P LOSS WILD-TYPE 663  75
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               306                738 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                 75 
$`18P LOSS MUTATED`
TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P 
      131.67        14.37        20.88        13.68        28.01        18.02 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
      101.98        55.43         5.19        67.33        34.55        25.22 
TCGA-A2-A0EN TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T4 
      134.40        34.29        31.82        63.29        50.43        20.52 
TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       20.75        18.21        21.90        49.48        19.33        48.46 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A25D 
       23.77        17.36        60.72        19.20        17.19        18.15 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A13F TCGA-A7-A26F 
       83.01        29.98        26.96        34.29        25.15        24.26 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       22.32        11.28        14.93        13.74        17.92        14.73 
TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07G 
       10.42        17.98        29.03        26.01        53.98        18.97 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L 
       10.98         9.99        15.06        38.01        37.05         9.99 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N 
       30.97        12.00        50.04        49.05        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H TCGA-AC-A2FF TCGA-AC-A2FM 
       25.02        14.01        19.04         5.72        55.43        26.04 
TCGA-AC-A2FO TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62V 
       50.70         2.27        32.45        16.57        19.79        11.44 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A04A 
        0.03        20.19         1.12         2.30         0.33         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FV 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M 
        0.36         0.33         0.30         0.33        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA 
       66.77        81.63        52.18        26.04        20.32        21.53 
TCGA-AO-A0JG TCGA-AO-A129 TCGA-AO-A12E TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       26.24       108.03        57.30        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U2 
        5.65        15.62        32.91        86.66        64.83        83.87 
TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R 
       61.84        39.98        61.28        63.62       160.90        87.22 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A5QM 
       85.35        50.96        73.18        58.92        93.83        54.74 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RH 
       16.04        10.59       176.98        18.77       110.14       189.01 
TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
       81.17       102.77       100.70        79.63        18.35       113.79 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 
       73.51       139.17        74.99        59.84        25.55        39.55 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ 
       56.94        37.22        18.21        48.69        45.57        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0GY 
       41.75        42.90        38.01        47.41         9.63        30.35 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY 
       24.56        23.08        52.96        20.38        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V 
       23.93         8.81        90.84        26.66        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY 
       69.93        91.99        42.28        12.00        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM 
       25.81        31.53        97.48        24.66        33.17        45.63 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 
       28.14        38.60        83.31       130.16        18.64        23.51 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 
       12.66        11.77        12.66        12.66         0.39         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
        1.12         1.05         4.08        12.33        10.92        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
        0.16        12.03         2.30         3.25         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Y 
        8.28         9.67         9.53         9.50         0.03        11.90 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD 
       13.97        21.14        14.17        17.49        16.50        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.90        12.03        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR 
       20.38        18.58        27.58        21.83        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 
       12.99        16.54        14.14        13.48        10.09        18.51 
TCGA-D8-A73U TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O 
       16.18        34.42        46.59        40.11        28.44        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A154 
       38.24        38.60        34.26        18.51        27.12        19.43 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD 
       14.79        25.05        20.71        11.05        60.53        17.10 
TCGA-E2-A1IH TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       33.73        20.98        28.90         8.75        43.04         5.52 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND 
       34.92        26.56        12.85        32.88        36.56        12.59 
TCGA-E9-A1NG TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E 
       25.84         2.76         6.58        21.27        35.64        12.89 
TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW 
        1.94         0.72        29.72        23.84         0.79        12.20 
TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC 
       18.90        25.94        29.85        52.96         7.86         6.15 
TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DH 
       14.43        55.00        25.91        10.16         7.40        72.10 
TCGA-GM-A2DL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 
      115.69        11.84        13.22         7.10        10.62        11.44 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 
       15.32        22.26        12.36        14.07        27.91        36.30 
TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       20.38        26.04        19.73        64.21        86.96         0.16 
TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A89A 
       16.50        16.93        15.39         3.81        29.03        16.04 

$`18P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        43.43        48.10        14.27        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y 
       78.41       121.94        73.84        87.25        63.12        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55        75.25        98.99       107.93        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        61.58       101.72        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       74.40        72.00        35.05        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        49.84        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       50.47        21.67        18.61        31.73        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV 
      105.34        10.59        20.88        39.65        33.93        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        21.30        23.21        21.14        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A4SE 
       10.29        13.41        14.70        11.97        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z 
       13.02        13.02         1.02        53.06        31.00         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       17.03         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       45.07        18.05        36.95        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       33.01        19.96        12.00        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
       33.01       112.08        43.00        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I 
       41.98        12.00         9.99         9.99         1.02        45.07 
TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       29.98         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        27.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        0.95         2.37        10.85         1.48        38.53        99.35 
TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN 
       40.57        36.99        38.79        33.04         0.92        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83        22.19        14.99        23.24        24.79         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        8.22         1.32         0.33         0.23         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        1.78         1.71         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         7.04 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03R 
        0.33         0.33         5.33         5.59        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 
       47.87        58.95        29.13        32.78        21.40        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        53.03        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       21.37        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78        90.58        98.27        64.04 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       70.39         0.53        17.79        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32        73.64         5.26        74.79        42.35        98.93 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       75.55        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX 
       43.56        43.07        17.23        37.81        76.21        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        2.76       104.28        97.84        76.01        53.36        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        89.00        78.48        72.76       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       40.54        20.38        20.45        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      112.37       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
       68.45       234.28        78.02       172.96       162.05       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX 
       89.46       131.21       157.41        97.48       188.68        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       43.59       101.52       170.17        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        24.53        20.45        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       39.16        48.36        56.98        51.68        32.02        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       24.85        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.69        53.95        49.94        11.67        44.02        48.13 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        23.44        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        24.49        31.00        24.43        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       37.78        35.51        41.00        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        12.89        51.32         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         2.01         7.23        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB 
        7.36       113.82        82.85        49.58        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A28O 
       72.07       144.59        72.07        26.14        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 
        6.44        20.12        10.52       109.28         8.94         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 
       11.77        11.77        12.66        12.66        12.66         3.16 
TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W 
        2.24         4.11        11.34        10.42         0.30         0.23 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        0.03        12.20         0.99         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       13.41        19.46        20.88        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JK 
       13.48        19.20        18.71        15.78        12.03        20.12 
TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.09        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        14.50        17.69        15.55        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        15.16        12.66        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.24        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       14.43         9.44        16.41         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X 
       12.53        12.26        33.37        21.67         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N 
       43.00        27.52        40.41        37.51        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       40.96        33.17        33.30        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       28.60        25.41        23.24        21.04        23.87        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II 
       28.50        16.47        38.30        37.41        32.78        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        22.19        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       27.42        39.62        19.66        24.59        40.47        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      106.75       102.61        16.93        15.72         8.28        30.61 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.29        34.82        36.82        13.48        12.00        13.12 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        35.77        35.24         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         6.12         3.02        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 
       32.09        40.24         1.12        34.65        34.59        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 
       23.51        20.71        17.06         0.69        27.22         7.13 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX 
       12.33        14.70        13.81        14.40        15.39        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       22.82        29.95        40.41        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       23.11        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        34.55        19.96        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        23.51       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM 
       83.34        75.02        70.85        85.15        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.43 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       11.57        21.24        13.28        24.95        10.95        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        14.70        14.47        14.79         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U 
       15.68         7.46        14.50        14.70        14.73        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        17.36        14.07        28.21 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG 
       40.11         8.91        47.01         0.26         9.93        13.12 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       16.80        13.84        15.35        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       17.03        11.41        52.96        15.35       108.07       107.05 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            189.01             234.28 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             21.68              25.02 
[1] "0.0 - 189.0 (21.7)" "0.0 - 234.3 (25.0)"
[1] "hr=" "2.2"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        25       23        0        0       100        69
  18P LOSS WILD-TYPE      64       58        8        3       253       176
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         47         16         25        6
  18P LOSS WILD-TYPE         2        103         13         38       14
                    vv
clus                 STAGE TIS STAGE X
  18P LOSS MUTATED           0       1
  18P LOSS WILD-TYPE         1      12
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  25                 64
  STAGE IA                 23                 58
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA               100                253
  STAGE IIB                69                176
  STAGE III                 0                  2
  STAGE IIIA               47                103
  STAGE IIIB               16                 13
  STAGE IIIC               25                 38
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of 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    68 186  38  22
  18P LOSS WILD-TYPE 204 430  92  18
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               68                204
  T2              186                430
  T3               38                 92
  T4               22                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED   141 100  39  27
  18P LOSS WILD-TYPE 360 250  78  48
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              141                360
  N1              100                250
  N2               39                 78
  N3               27                 48
[1] 4 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
  18P LOSS MUTATED   260   6
  18P LOSS WILD-TYPE 619  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    260    6
  18P LOSS WILD-TYPE  619   15
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              260                619
  1                6                 15
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   311   3
  18P LOSS WILD-TYPE 740   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    311    3
  18P LOSS WILD-TYPE  740    8
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              311                740
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P LOSS MUTATED                            0                           246
  18P LOSS WILD-TYPE                          1                           517
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P LOSS MUTATED                               46                   3
  18P LOSS WILD-TYPE                            146                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P LOSS MUTATED                       2                                6
  18P LOSS WILD-TYPE                     2                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18P LOSS MUTATED                    0             11
  18P LOSS WILD-TYPE                 17             37
D73V8, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 246                517
  INFILTRATING LOBULAR CARCINOMA                 46                146
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 24
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                 11                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    85 229
  18P LOSS WILD-TYPE 203 545
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     85  229
  18P LOSS WILD-TYPE  203  545
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                85                203
  YES              229                545
[1] 2 2
[1] FALSE
D73V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0    27
  18P LOSS WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          50   209
  18P LOSS WILD-TYPE                       120   527
D73V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          27                 33
  BLACK OR AFRICAN AMERICAN                      50                120
  WHITE                                         209                527
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    11 257
  18P LOSS WILD-TYPE  27 601
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11  257
  18P LOSS WILD-TYPE   27  601
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 27
  NOT HISPANIC OR LATINO              257                601
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   262  46
  18Q LOSS WILD-TYPE 654  82
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               308                736 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                46                 82 
$`18Q LOSS MUTATED`
TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
      131.67        14.37        20.88        28.01        18.02       101.98 
TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EU 
       55.43         5.19       107.93        67.33       134.40        34.29 
TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YE 
       31.82        27.12        50.43        20.52        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       21.90        49.48        19.33        48.46        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XT 
       60.72        19.20        42.44        17.19        18.15        83.01 
TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F 
       29.98        26.96        34.29        35.67        31.73        25.15 
TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       24.26        22.32        11.28        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06R 
       17.92        14.73        12.10        10.29        10.42        17.98 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G 
       29.03        26.01         1.02        17.03        53.98        18.97 
TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
        9.99        15.06        38.01        37.05        31.00         0.99 
TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M 
       30.97         9.99        12.00        50.04        49.05        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H 
        1.02        25.02         0.99        14.01        19.04         5.72 
TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 
       55.43        26.04         2.27        32.45        16.57        19.79 
TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS 
       11.44        12.26         0.03        20.19         1.12         2.30 
TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FL 
        0.33         2.96         7.36         6.51         0.16         7.59 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XU TCGA-AO-A03L 
        0.33         0.36         0.33         0.30         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A129 
       66.77        32.78        52.18        20.32        21.53       108.03 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       64.04        57.30        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
        5.65        15.62        32.91        74.79        86.66        98.93 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H 
      101.95        83.87        39.98        61.28        63.62       160.90 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A251 
       87.22        97.84        85.35        50.96        89.00        78.48 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0IK 
       73.18        58.92        20.38        54.74        10.59        18.77 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RS 
      110.14       211.56       189.01        81.17       102.77       100.70 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       79.63        18.35       113.79       101.52        73.51       170.17 
TCGA-B6-A402 TCGA-BH-A0AZ TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG 
       74.99        28.50        56.94        37.22        18.21        24.85 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DH 
       48.69        45.57        11.67        49.05        42.90        38.01 
TCGA-BH-A0DQ TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI 
        3.22        30.35        23.08        41.00        52.96        20.38 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18U 
       12.89        27.25        23.93         8.81        90.84        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY 
       51.16        69.93        91.99        42.28        12.00        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 
       25.81        31.53        97.48        24.66        45.63        28.14 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12P TCGA-C8-A12Q 
       83.31       130.16        23.51        18.87        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66         0.39         1.87         1.05         4.08        12.33 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y 
       11.28         0.16        12.03         2.30         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 
        8.28         9.67         9.53         0.03         9.50         0.03 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.88        13.97        21.14        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR 
       20.38        18.58        27.58        21.83        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 
       12.99        16.54        14.14        13.48        10.09        18.51 
TCGA-D8-A73U TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O 
       16.18        34.42        46.59        40.11        28.44        44.68 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A 
       18.51        25.41        27.12        19.43        25.05        23.34 
TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IO 
       20.71        11.05        60.53        17.10        33.73        20.98 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 TCGA-E2-A574 
       28.90         8.75        43.04         5.52        34.92        26.56 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1R6 TCGA-E9-A1RF 
       12.85        32.88        36.56        12.59         2.76         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS 
       21.27        35.64        12.89         1.94         0.72        29.72 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OY 
       23.84         0.79        12.20        18.90        25.94        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR 
       40.41        52.96         7.86         6.15        14.43        55.00 
TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A2DL 
       25.91        10.16         7.40       109.87        72.10       115.69 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
        2.60        11.84        13.22        10.62        11.44        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.32        14.47        22.26        16.08        14.07        27.91 
TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC 
       36.30        20.38        26.04        28.21        19.73        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-UU-A93S 
       64.21        86.96         0.16        16.50        16.93         3.81 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`18Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
       88.60       107.93        75.55        75.25        98.99        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       34.55        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW 
      107.61        79.76        74.40        72.00        35.05        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       24.72        63.29        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        49.84        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM 
       32.55        25.28        50.47        21.67        18.61        31.73 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       23.47        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
      107.70       105.34        10.59        20.88        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        47.31        34.98        50.37        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G 
       29.79        20.19        23.61        29.56        31.36        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        21.73        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.41        14.70        11.97        14.50        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T 
        9.37         8.75        13.02        13.02         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       31.00         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       24.99        45.07        18.05        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        12.00         9.99        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
       33.01       112.08        43.00        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       41.98        12.00         9.99         1.02        45.07        29.98 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 
        8.98        19.04        15.02        12.00        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG 
       10.85         1.48        38.53        99.35        40.57        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70        33.04         0.92        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
       22.19        14.99        23.24        24.79         1.55        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
       17.42        18.67        13.58         1.68         8.22         1.32 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        9.96         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX 
        7.96         7.00         7.17         6.28         7.04         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33         5.59        61.35        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 
       68.75        47.87        58.95        29.13        21.40        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       37.48        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       102.58        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       61.87        70.39         0.53        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
      111.32        73.64         5.26        42.35        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      107.24        65.36       114.02        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY 
       43.07        17.23        37.81        76.21        62.14        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22        96.89        78.51        84.20         2.76 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A254 
      104.28        76.01        53.36        83.77        79.00        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       143.21        20.25        62.86        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       52.11        38.17        39.39        40.54        16.04        20.45 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37       176.98       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
       84.59       110.93       140.88        68.45       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      172.96       162.05       140.48        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        21.47       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A401 
       28.27        68.94        58.88        43.59       139.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       68.12       103.63        71.15        24.53        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       56.98        51.68        32.02        25.71        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        35.67        27.19        53.69        53.95        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        44.02        48.13        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       24.56        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       51.32        50.79         5.59        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
       23.05         2.01         7.23        20.12        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB 
      113.82        82.85        55.69        49.58        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07       144.59        72.07        26.14        38.60 
TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       57.83        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 
        8.94        18.64         9.63         5.26         9.70        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66         3.16         2.24         1.12         4.11 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       10.92        11.34        10.42         3.25         0.30         0.23 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       12.20         0.99         0.23        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       19.46        11.90        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL 
       19.20        18.71        18.15        12.03        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       19.40        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        14.50        17.69        15.55        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        15.16        12.66        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.24        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       14.43         9.44        16.41         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X 
       12.53        12.26        33.37        21.67         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N 
       43.00        27.52        40.41        37.51        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 
       34.26        32.02        31.96        28.60        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       23.87        14.79        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       12.92        17.42        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        17.06        14.07        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        16.47        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX 
       40.47        18.87       106.75       102.61        16.93        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 
        8.28        30.61        34.29        34.82        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       12.00        13.12        39.55        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02        21.21        32.09        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.65        34.59        34.13        32.05        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        41.03        23.51        20.71        17.06 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69        27.22         7.13        24.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO 
       18.41        30.18        15.72        12.33        14.70        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       14.40        15.39        39.72         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 
       16.57        15.68        28.77        22.82        29.95        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS 
       19.99        13.94        10.52        34.55        19.96        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA 
       22.09        34.03        17.49        23.51        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        85.15        86.96 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 
       11.57        21.24         7.10        13.28        24.95        10.95 
TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       25.05        14.70        14.79         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        14.70        12.36        14.73        22.39         2.10 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C 
       41.92        42.77        17.36        14.07        40.11         8.91 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        13.12        16.80        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G 
       15.35        14.96        13.84        13.94        17.03        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        15.35       108.07       107.05 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            211.56             234.28 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            21.155             25.630 
[1] "0.0 - 211.6 (21.2)" "0.2 - 234.3 (25.6)"
[1] "hr=" "1.6"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        23       26        0        0        98        67
  18Q LOSS WILD-TYPE      66       55        8        3       255       178
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         49         16         25        6
  18Q LOSS WILD-TYPE         2        101         13         38       14
                    vv
clus                 STAGE TIS STAGE X
  18Q LOSS MUTATED           0       3
  18Q LOSS WILD-TYPE         1      10
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  23                 66
  STAGE IA                 26                 55
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                98                255
  STAGE IIB                67                178
  STAGE III                 0                  2
  STAGE IIIA               49                101
  STAGE IIIB               16                 13
  STAGE IIIC               25                 38
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    69 189  37  20
  18Q LOSS WILD-TYPE 203 427  93  20
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               69                203
  T2              189                427
  T3               37                 93
  T4               20                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED   144  94  43  28
  18Q LOSS WILD-TYPE 357 256  74  47
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              144                357
  N1               94                256
  N2               43                 74
  N3               28                 47
[1] 4 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
  18Q LOSS MUTATED   257   6
  18Q LOSS WILD-TYPE 622  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    257    6
  18Q LOSS WILD-TYPE  622   15
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              257                622
  1                6                 15
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   313   3
  18Q LOSS WILD-TYPE 738   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    313    3
  18Q LOSS WILD-TYPE  738    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              313                738
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q LOSS MUTATED                            1                           244
  18Q LOSS WILD-TYPE                          0                           519
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q LOSS MUTATED                               50                   2
  18Q LOSS WILD-TYPE                            142                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q LOSS MUTATED                       2                                6
  18Q LOSS WILD-TYPE                     2                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18Q LOSS MUTATED                    0             11
  18Q LOSS WILD-TYPE                 17             37
D74V8, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 244                519
  INFILTRATING LOBULAR CARCINOMA                 50                142
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 24
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                 11                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    90 226
  18Q LOSS WILD-TYPE 198 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     90  226
  18Q LOSS WILD-TYPE  198  548
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                90                198
  YES              226                548
[1] 2 2
[1] FALSE
D74V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0    24
  18Q LOSS WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          53   207
  18Q LOSS WILD-TYPE                       117   529
D74V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                 36
  BLACK OR AFRICAN AMERICAN                      53                117
  WHITE                                         207                529
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    12 258
  18Q LOSS WILD-TYPE  26 600
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12  258
  18Q LOSS WILD-TYPE   26  600
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 26
  NOT HISPANIC OR LATINO              258                600
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   161  25
  19P LOSS WILD-TYPE 755 103
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               186                858 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                103 
$`19P LOSS MUTATED`
TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04T 
       42.81         9.96        13.68        18.21        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EO 
       87.25        55.43        24.79       107.93        25.22        80.28 
TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW 
       49.84        20.75        21.90        21.67        23.77        17.36 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E 
       83.01        47.31        50.37        26.96        31.73        20.19 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q 
       21.73        14.50        17.92        14.73        10.42         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L 
       17.98        53.06        17.03        53.98        18.97        32.05 
TCGA-A8-A07O TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        9.99         9.99        33.01        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N 
       31.00        33.01         9.99         1.02        45.07         1.02 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A8OQ 
       99.35        26.04        33.04        11.44        12.26         1.12 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ 
        0.23         2.96         0.33         7.04         0.33         0.33 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD 
       61.35        66.77        95.70        21.40        52.18        72.00 
TCGA-AO-A0JM TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TQ 
       71.80        61.87        17.79         5.65         2.56        73.64 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ 
       74.79        98.93        83.87       114.02        52.77        43.07 
TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LK 
      160.90        87.22        97.84        89.00        73.18        54.21 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A1KF TCGA-B6-A1KN 
       10.59        77.62       129.57       110.14       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BG TCGA-BH-A0BT 
       74.99        68.12        59.84        39.55        24.85        45.57 
TCGA-BH-A0BW TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EB TCGA-BH-A0H0 TCGA-BH-A0H7 
       11.67         3.22         4.41        24.49        15.16        23.08 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18L 
       27.25        50.79        23.05         8.81         7.23        26.66 
TCGA-BH-A18S TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A204 
       66.05        12.00        24.66        72.07        72.07        83.31 
TCGA-BH-A209 TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z 
      130.16        11.77        11.77        12.66        12.66         0.39 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN 
        1.05         4.08        10.92        12.03        10.42         3.25 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ 
        0.43         8.28        12.20        13.02        12.49        19.46 
TCGA-D8-A13Y TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA 
       11.90        15.78        18.97        20.09        19.40        27.58 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 
       16.41         6.35        16.54        14.14        13.48        46.59 
TCGA-E2-A14O TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ 
       44.68        27.12        25.05        12.92        14.07        60.53 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 
       34.92        26.56        13.48         9.86        11.90         2.56 
TCGA-E9-A1RC TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A2JS 
       40.24        34.59        34.13        41.03        23.51        29.72 
TCGA-E9-A5UO TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P8 
       13.81        25.94        22.82        29.95        40.41         7.86 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 
       18.90         6.15        19.96        55.00        52.73        17.49 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5D7 
       83.34        72.10        22.26        12.36        22.39        58.52 
TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 TCGA-WT-AB44 
       20.38        28.21         0.16        16.50        14.96        29.03 

$`19P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      104.81        78.41       121.94        63.12       101.98        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19        98.99        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       34.55        33.76        61.58       101.72       134.40       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       79.76        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        60.72        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
      105.34        10.59        20.88        39.65        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        49.48        34.98        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       13.74        21.17        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X 
        9.37         8.75        13.02        13.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       14.01        12.00        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       45.07        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       38.01        28.96         9.99        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       43.00        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
       12.00         9.99        12.00        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        38.53        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        50.70         0.92         2.27        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19        14.99        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55        13.71        17.42        18.67        13.58 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22         0.03        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        80.28        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       58.95        29.13        32.78        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 
       21.37        26.24        50.24        62.04        55.33       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62        70.39         0.53        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR 
       15.62        32.52        32.91        19.20       111.32         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       86.66        42.35        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
      101.95        85.97        75.55        61.84        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       76.11        43.73        43.56        39.98        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       76.21        61.28        63.62        62.14        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22        96.89        78.51        84.20         2.76       104.28 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       20.38        54.74        16.04        20.45       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       220.90        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88        43.59        73.51       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      103.63        71.15        24.53        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       46.95        40.83        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        49.94        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        48.23        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        47.41        16.27        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       10.78        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        51.32         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
       44.81         2.01        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       30.28        55.63        37.55         7.36        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       69.93        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       63.35        55.00        45.63       144.59        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        57.83        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28         8.94        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.87         1.12         4.11        12.33        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 
        0.16         2.30         0.30         0.23         0.36         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         0.03         9.50         0.99         0.03         0.23 
TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       13.41        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69        15.55        15.85        16.31 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        12.66        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
        9.44        16.41         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
        8.02        12.10        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       32.02        31.96        28.60        18.51        25.41        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        21.63        18.21        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        13.02        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         8.28        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       34.29        12.85        34.82        32.88        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       25.84        28.27        34.95         6.12         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       21.21        32.09        32.09         1.12        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       21.27        35.64        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       22.75        12.89        20.71        17.06         0.69        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56         0.72         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41        30.18        15.72        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       34.55        25.91        22.09        34.03        10.16        23.51 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
        7.40       109.87        59.57       216.76        79.10        75.02 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        14.79         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        14.70        14.73        14.07        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        13.12        16.93        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       13.84        15.35        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        52.96        15.35        16.04       108.07       107.05 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            160.90             234.28 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            22.935             24.755 
[1] "0.2 - 160.9 (22.9)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED        16       11        1        0        61        45
  19P LOSS WILD-TYPE      73       70        7        3       292       200
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         27          5         12        6
  19P LOSS WILD-TYPE         1        123         24         51       14
                    vv
clus                 STAGE TIS STAGE X
  19P LOSS MUTATED           0       2
  19P LOSS WILD-TYPE         1      11
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  16                 73
  STAGE IA                 11                 70
  STAGE IB                  1                  7
  STAGE II                  0                  3
  STAGE IIA                61                292
  STAGE IIB                45                200
  STAGE III                 1                  1
  STAGE IIIA               27                123
  STAGE IIIB                5                 24
  STAGE IIIC               12                 51
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    41 118  20   8
  19P LOSS WILD-TYPE 231 498 110  32
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               41                231
  T2              118                498
  T3               20                110
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P LOSS MUTATED    79  71  18  15
  19P LOSS WILD-TYPE 422 279  99  60
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               79                422
  N1               71                279
  N2               18                 99
  N3               15                 60
[1] 4 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
  19P LOSS MUTATED   156   6
  19P LOSS WILD-TYPE 723  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    156    6
  19P LOSS WILD-TYPE  723   15
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              156                723
  1                6                 15
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   185   2
  19P LOSS WILD-TYPE 866   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    185    2
  19P LOSS WILD-TYPE  866    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              185                866
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P LOSS MUTATED                            0                           162
  19P LOSS WILD-TYPE                          1                           601
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P LOSS MUTATED                                8                   1
  19P LOSS WILD-TYPE                            184                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P LOSS MUTATED                       1                                4
  19P LOSS WILD-TYPE                     3                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19P LOSS MUTATED                    4              6
  19P LOSS WILD-TYPE                 13             42
D75V8, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 162                601
  INFILTRATING LOBULAR CARCINOMA                  8                184
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                  6                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    55 132
  19P LOSS WILD-TYPE 233 642
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     55  132
  19P LOSS WILD-TYPE  233  642
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                55                233
  YES              132                642
[1] 2 2
[1] FALSE
D75V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0    16
  19P LOSS WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          41   109
  19P LOSS WILD-TYPE                       129   627
D75V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                 44
  BLACK OR AFRICAN AMERICAN                      41                129
  WHITE                                         109                627
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8 146
  19P LOSS WILD-TYPE  30 712
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8  146
  19P LOSS WILD-TYPE   30  712
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 30
  NOT HISPANIC OR LATINO              146                712
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   134  23
  19Q LOSS WILD-TYPE 782 105
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               157                887 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                105 
$`19Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SQ TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D1 
        9.96        18.21        87.25        55.43        24.79        34.55 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW 
       80.28        27.12        20.75        21.90        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A13E TCGA-A7-A2KD TCGA-A7-A56D TCGA-A8-A06Q 
       19.20        83.01        20.19        22.32        14.73         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       17.98        53.06        53.98        18.97        32.05         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A 
       33.01        19.96        12.00        31.00        33.01         9.99 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-AC-A23C TCGA-AC-A2BM 
        1.02        45.07        33.07         1.02         0.95        99.35 
TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS 
       26.04        11.44         1.12         0.23         2.96         0.33 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        7.04         0.33         0.33        80.28        66.77        95.70 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A1KQ 
       21.40        52.18        72.00        55.33        71.80        61.87 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ 
       17.79        24.79         5.65        83.87       114.02        52.77 
TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A252 TCGA-AR-A2LK 
       43.07       160.90        87.22        97.84        73.18        54.21 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A1KN 
       10.59        77.62       129.57        21.47       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DQ 
       74.99        68.12        45.57        41.75        42.90         3.22 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0WA 
       24.49        31.00        15.16        23.08        50.79        23.05 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18S TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A209 
        8.81         7.23        66.05        72.07        83.31       130.16 
TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z 
       18.64        11.77        11.77        12.66        12.66         0.39 
TCGA-C8-A1HF TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A 
       10.92        10.42         0.36         0.43         9.50        12.20 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ 
       12.49        19.46        11.90        15.78        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 
       19.40        27.58        16.41         6.35        16.54        14.14 
TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S 
       13.48        46.59        44.68        25.05        12.92        14.07 
TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI 
       60.53        34.92        26.56        13.48        35.24         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A226 
       11.90         2.56        21.21        32.09        34.59        34.13 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A5UO TCGA-EW-A1OW 
       41.03        23.51         0.69        29.72        13.81        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FR TCGA-EW-A2FS 
       29.95        40.41        18.90         6.15        55.00        52.73 
TCGA-EW-A3U0 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-LL-A7T0 TCGA-OL-A5D7 
       17.49        83.34        70.85        72.10        12.36        58.52 
TCGA-OL-A5RY TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 TCGA-UU-A93S 
       24.72        28.21         0.16        16.50        14.96         3.81 
TCGA-WT-AB44 
       29.03 

$`19Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        19.20       104.81        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        63.12       101.98        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
        5.19        98.99       107.93        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58        25.22       101.72       134.40       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        18.90        32.55        25.28        18.21        50.47 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X 
       10.42         8.75        13.02        13.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        17.03         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       18.97        14.01        12.00        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L 
       13.02         0.99        38.01        28.96        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       30.97        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       50.04        49.05        29.98        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E 
       21.04         0.99        27.02        17.03        38.04         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         5.72         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        50.70        33.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
       32.45        16.31        14.83        22.19        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
       20.19         1.32         2.30         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         1.78         1.71         9.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX 
        7.00         7.59         7.17         6.28         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       62.04       102.58        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J 
       28.37        14.73        82.62        70.39         0.53        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
      130.09        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      111.32        73.64         5.26        74.79        86.66        42.35 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       101.95 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       85.97        75.55        61.84        51.25        48.82        76.11 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       61.28        63.62        62.14        33.73        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T 
       96.89        78.51        84.20         2.76       104.28        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       20.38        54.74        16.04        20.45       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       220.90        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88        43.59        73.51       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        24.53        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        44.02        48.13        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        30.35        10.78        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        27.25         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J 
       23.93        24.95        42.35        44.81         2.01        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       63.35        55.00        45.63        72.07       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       26.14        38.60        57.83        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28         8.94        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87         1.12         1.05         4.11         4.08        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34        11.28         0.16        12.03         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.30         0.23         8.28         9.67         9.53         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Z 
        0.99         0.03         0.23        13.02        13.41        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD 
       19.20        14.17        17.49        16.50        18.71        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        12.03        12.03        14.01        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV 
       17.69        15.55        15.85        16.31        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.66        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       43.00        34.42        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        18.51        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
       20.58        11.05        13.02        19.56        17.06        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       16.93         5.52        15.72         8.28        30.61        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       12.85        34.82        32.88        36.82        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 
       36.56        39.55        12.59        35.77        25.84        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC 
       34.95         6.12         3.02         2.76        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
        1.12        34.65         6.58        21.27        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06        27.22         1.94         7.13        24.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        14.70         0.79        14.40        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        28.77        25.94        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       52.96        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       25.91        22.09        34.03        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI 
      109.87        59.57       216.76        79.10        75.02        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.43        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        14.70        14.73        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        22.32        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        13.12        16.93        16.80        15.39 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G 
       13.84        15.35        13.84        13.94        17.03        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        15.35        16.04       108.07       107.05 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            160.90             234.28 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             23.05              24.72 
[1] "0.2 - 160.9 (23.1)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED        10       11        0        0        54        37
  19Q LOSS WILD-TYPE      79       70        8        3       299       208
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           1         26          3          7        6
  19Q LOSS WILD-TYPE         1        124         26         56       14
                    vv
clus                 STAGE TIS STAGE X
  19Q LOSS MUTATED           0       2
  19Q LOSS WILD-TYPE         1      11
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 11                 70
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                54                299
  STAGE IIB                37                208
  STAGE III                 1                  1
  STAGE IIIA               26                124
  STAGE IIIB                3                 26
  STAGE IIIC                7                 56
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of 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    38  99  15   5
  19Q LOSS WILD-TYPE 234 517 115  35
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               38                234
  T2               99                517
  T3               15                115
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    64  60  21  10
  19Q LOSS WILD-TYPE 437 290  96  65
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               64                437
  N1               60                290
  N2               21                 96
  N3               10                 65
[1] 4 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
  19Q LOSS MUTATED   126   6
  19Q LOSS WILD-TYPE 753  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    126    6
  19Q LOSS WILD-TYPE  753   15
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              126                753
  1                6                 15
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   155   2
  19Q LOSS WILD-TYPE 896   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    155    2
  19Q LOSS WILD-TYPE  896    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE              155                896
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q LOSS MUTATED                            0                           137
  19Q LOSS WILD-TYPE                          1                           626
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q LOSS MUTATED                                5                   1
  19Q LOSS WILD-TYPE                            187                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q LOSS MUTATED                       0                                4
  19Q LOSS WILD-TYPE                     4                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19Q LOSS MUTATED                    4              5
  19Q LOSS WILD-TYPE                 13             43
D76V8, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 137                626
  INFILTRATING LOBULAR CARCINOMA                  5                187
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                  5                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    52 105
  19Q LOSS WILD-TYPE 236 669
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     52  105
  19Q LOSS WILD-TYPE  236  669
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                52                236
  YES              105                669
[1] 2 2
[1] FALSE
D76V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0    13
  19Q LOSS WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          33    93
  19Q LOSS WILD-TYPE                       137   643
D76V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                 47
  BLACK OR AFRICAN AMERICAN                      33                137
  WHITE                                          93                643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 125
  19Q LOSS WILD-TYPE  33 733
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  125
  19Q LOSS WILD-TYPE   33  733
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 33
  NOT HISPANIC OR LATINO              125                733
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    76  14
  20P LOSS WILD-TYPE 840 114
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                90                954 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                114 
$`20P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0YE TCGA-A2-A3XU TCGA-A2-A4S3 
        9.96        31.79        73.84        18.21        29.98        21.90 
TCGA-A7-A0CE TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A079 
       35.31        31.36        21.73        21.17         1.02         9.01 
TCGA-A8-A07L TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A3W5 
       32.05        33.01         9.99        31.00        17.03        16.57 
TCGA-AC-A62X TCGA-AN-A0AM TCGA-AN-A0XW TCGA-AO-A0J6 TCGA-AO-A1KT TCGA-AQ-A04J 
       13.71         0.16         5.59        37.48        17.79        26.93 
TCGA-AQ-A54N TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 
        2.56       107.24       114.02        17.23        50.89        78.48 
TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0X1 
       12.13       176.98        18.77        81.17       100.70       186.48 
TCGA-B6-A1KN TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BR TCGA-BH-A0DH 
      139.17        59.84        39.16        51.68        53.69        38.01 
TCGA-BH-A0E1 TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FM TCGA-C8-A12M 
       15.68        51.16       114.15        33.17        45.63        11.77 
TCGA-C8-A134 TCGA-C8-A8HQ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XA 
        1.12        12.49        20.12        20.09        19.40        27.58 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H 
       21.83        14.50        16.41        14.14        16.04        13.05 
TCGA-D8-A27R TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A2P5 
       10.09        47.15        38.60        23.34        20.71        16.93 
TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A22G 
       34.92        36.82        39.55         2.76        34.65        23.51 
TCGA-E9-A244 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3U0 
        0.69        29.82         7.86        55.00        22.09        17.49 
TCGA-EW-A423 TCGA-GM-A2DF TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW 
       10.16        70.85        11.57        14.79        22.39        36.36 
TCGA-OL-A5S0 TCGA-OL-A66O TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-AA0Z TCGA-WT-AB44 
       20.38        17.36        28.21         0.16        16.80        29.03 

$`20P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        78.41       121.94 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       75.55        75.25         5.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       107.61        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       18.90        20.75        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        83.01        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.14        38.30        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E 
       37.45        35.67        33.11        29.79        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       25.15        23.61        29.56        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
        9.37        10.42         8.75        13.02        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        45.07        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        38.01        28.96        19.96        12.00        37.05 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       21.04         0.99        27.02        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       14.99        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L 
        0.33         0.33         0.33         0.33         5.33        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
        0.53        24.79       130.09         5.65        15.62        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       86.66        42.35        98.93        64.83        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      101.95        83.87        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        76.11        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28        87.22        97.84        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       85.35        50.96        83.77        79.00        89.00        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       143.21        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       112.37       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       211.56        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52        73.51       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       68.12       103.63        71.15        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.55        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       56.98        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       55.63        37.55        66.05         7.36        51.39        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66       120.62        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28         8.94        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66         0.39         3.16         2.24 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.87         1.05         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.03         0.23        13.02        13.41        19.46        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       18.97        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       18.15        12.39        17.16        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        15.55        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.24        17.42        13.45        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         0.76        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18         8.02        12.10 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        18.51        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04         5.52        15.72         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 
       26.56        34.29        12.85        34.82        32.88        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        36.56        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        6.12         3.02        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       12.89        20.71        17.06        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        15.72        12.33        23.84        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       13.81        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 
       19.96        52.73        25.91        34.03        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        41.92        42.77        26.04        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        16.50        13.12        16.93        15.39        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.35        14.96        13.84        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        52.96        15.35        16.04       108.07       107.05 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.16               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            186.48             234.28 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            21.995             24.690 
[1] "0.2 - 186.5 (22.0)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         3        6        0        0        37        19
  20P LOSS WILD-TYPE      86       75        8        3       316       226
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0         14          3          6        4
  20P LOSS WILD-TYPE         2        136         26         57       16
                    vv
clus                 STAGE TIS STAGE X
  20P LOSS MUTATED           0       0
  20P LOSS WILD-TYPE         1      13
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   3                 86
  STAGE IA                  6                 75
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                37                316
  STAGE IIB                19                226
  STAGE III                 0                  2
  STAGE IIIA               14                136
  STAGE IIIB                3                 26
  STAGE IIIC                6                 57
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of 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    16  64   8   4
  20P LOSS WILD-TYPE 256 552 122  36
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               16                256
  T2               64                552
  T3                8                122
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    41  30  11   8
  20P LOSS WILD-TYPE 460 320 106  67
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               41                460
  N1               30                320
  N2               11                106
  N3                8                 67
[1] 4 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
  20P LOSS MUTATED    72   5
  20P LOSS WILD-TYPE 807  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     72    5
  20P LOSS WILD-TYPE  807   16
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               72                807
  1                5                 16
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    91   1
  20P LOSS WILD-TYPE 960  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     91    1
  20P LOSS WILD-TYPE  960   10
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               91                960
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P LOSS MUTATED                            0                            75
  20P LOSS WILD-TYPE                          1                           688
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P LOSS MUTATED                                8                   2
  20P LOSS WILD-TYPE                            184                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P LOSS MUTATED                       0                                2
  20P LOSS WILD-TYPE                     4                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20P LOSS MUTATED                    1              4
  20P LOSS WILD-TYPE                 16             44
D77V8, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  75                688
  INFILTRATING LOBULAR CARCINOMA                  8                184
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  4                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    28  64
  20P LOSS WILD-TYPE 260 710
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     28   64
  20P LOSS WILD-TYPE  260  710
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                28                260
  YES               64                710
[1] 2 2
[1] FALSE
D77V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     5
  20P LOSS WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                          23    56
  20P LOSS WILD-TYPE                       147   680
D77V11, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      23                147
  WHITE                                          56                680
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  70
  20P LOSS WILD-TYPE  33 788
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   70
  20P LOSS WILD-TYPE   33  788
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 33
  NOT HISPANIC OR LATINO               70                788
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    44   8
  20Q LOSS WILD-TYPE 872 120
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                52                992 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                120 
$`20Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A2-A3XU TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A26E TCGA-A7-A26I 
       31.79        29.98        35.31        35.67        31.36        21.73 
TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A62X 
        9.37         1.02        43.00        31.00        17.03        13.71 
TCGA-AN-A0AR TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A0J6 TCGA-AO-A1KS TCGA-AQ-A04J 
        0.33         5.59        95.70        37.48         0.53        26.93 
TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-B6-A0RS 
        2.56       114.02        17.23        50.89        78.48       100.70 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A18V TCGA-BH-A1FC TCGA-C8-A12M TCGA-C8-A27B 
      186.48        59.84        51.16       114.15        11.77         0.99 
TCGA-C8-A8HQ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-E2-A14N 
       12.49        20.12        20.09        21.83        14.50        47.15 
TCGA-E2-A15E TCGA-E2-A2P5 TCGA-E9-A1NC TCGA-E9-A22G TCGA-EW-A1P4 TCGA-EW-A1P8 
       20.71        16.93        39.55        23.51        29.82         7.86 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW 
       22.09        17.49        11.57        14.79        22.39        36.36 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-S3-AA0Z TCGA-WT-AB44 
       17.36        28.21        16.80        29.03 

$`20Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        13.68         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        48.46        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV 
       10.59        20.88        39.65        33.93        83.01        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        47.31        34.98        50.37        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       29.79        31.73        20.19        25.15        23.61        29.56 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02        13.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       26.01         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       21.04         0.99        27.02        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         5.72         1.48        38.53        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.99        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       11.44        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         6.51         0.16 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79       130.09         5.65        15.62        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       111.32        73.64         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        42.35        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        43.07        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        33.73       160.90        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        54.21        66.15        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      162.05       102.77       140.48        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.57       129.70        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
      101.52        73.51       139.17       170.17        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       68.12       103.63        71.15        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        9.44        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        2.24         1.87         1.12         1.05         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ 
       12.20         0.03         0.23        13.02        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        19.92        17.69        15.55        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       40.41        37.51        40.11        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        18.51        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       25.05        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         8.28        30.61        34.92        26.56 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        12.85        34.82        32.88        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        36.56        12.59        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        11.90        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02         2.76        21.21        32.09        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        41.03        12.89        20.71        17.06         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         7.13        24.56         0.72        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41        30.18        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        14.70         0.79        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 
       29.85        40.41        41.13        39.78        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       25.91        34.03        10.16        23.51         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.43        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        14.70        12.36        14.73        14.07        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P 
       23.47        65.62        41.92        42.77        26.04        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        16.50        13.12        16.93 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       15.39        13.84        15.35        14.96        13.84        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        11.41        52.96        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.33               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            186.48             234.28 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            22.240             24.575 
[1] "0.3 - 186.5 (22.2)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         1        2        0        0        26        13
  20Q LOSS WILD-TYPE      88       79        8        3       327       232
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          7          1          2        2
  20Q LOSS WILD-TYPE         2        143         28         61       18
                    vv
clus                 STAGE TIS STAGE X
  20Q LOSS MUTATED           0       0
  20Q LOSS WILD-TYPE         1      13
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   1                 88
  STAGE IA                  2                 79
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                26                327
  STAGE IIB                13                232
  STAGE III                 0                  2
  STAGE IIIA                7                143
  STAGE IIIB                1                 28
  STAGE IIIC                2                 61
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     7  41   5   1
  20Q LOSS WILD-TYPE 265 575 125  39
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                7                265
  T2               41                575
  T3                5                125
  T4                1                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED    28  18   5   3
  20Q LOSS WILD-TYPE 473 332 112  72
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               28                473
  N1               18                332
  N2                5                112
  N3                3                 72
[1] 4 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
  20Q LOSS MUTATED    43   2
  20Q LOSS WILD-TYPE 836  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     43    2
  20Q LOSS WILD-TYPE  836   19
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               43                836
  1                2                 19
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    54   0
  20Q LOSS WILD-TYPE 997  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     54    0
  20Q LOSS WILD-TYPE  997   11
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               54                997
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q LOSS MUTATED                            0                            39
  20Q LOSS WILD-TYPE                          1                           724
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q LOSS MUTATED                                7                   3
  20Q LOSS WILD-TYPE                            185                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q LOSS MUTATED                       0                                1
  20Q LOSS WILD-TYPE                     4                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20Q LOSS MUTATED                    1              3
  20Q LOSS WILD-TYPE                 16             45
D78V8, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  39                724
  INFILTRATING LOBULAR CARCINOMA                  7                185
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           0                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  3                 45
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    16  38
  20Q LOSS WILD-TYPE 272 736
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     16   38
  20Q LOSS WILD-TYPE  272  736
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                16                272
  YES               38                736
[1] 2 2
[1] FALSE
D78V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     5
  20Q LOSS WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                          15    29
  20Q LOSS WILD-TYPE                       155   707
D78V11, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      15                155
  WHITE                                          29                707
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4  42
  20Q LOSS WILD-TYPE  34 816
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   42
  20Q LOSS WILD-TYPE   34  816
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO               42                816
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   153  22
  21Q LOSS WILD-TYPE 763 106
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               175                869 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                22                106 
$`21Q LOSS MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-5L-AAT1 TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A0CW 
      131.67        42.81        48.36        39.32        73.84       107.93 
TCGA-A2-A0D0 TCGA-A2-A0EU TCGA-A2-A0SU TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FV 
       67.33        34.29        54.64        18.61        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A7-A0CJ TCGA-A7-A26G 
       17.36        42.44        34.98        38.37        30.61        23.74 
TCGA-A7-A4SD TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A08F TCGA-A8-A08G 
       14.50        13.02        29.03         9.01        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09B 
       12.00        37.05        31.00        33.01         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 
       45.07        25.02         8.98        19.04        13.02        27.02 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A04A 
       38.53        99.35         8.22        20.19         1.12         2.96 
TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XS 
        1.78         0.16         5.65         7.96         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 
        0.33        80.28        95.70        68.75        21.40        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TT 
       20.32        72.00       130.09         5.65       111.32        86.66 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A24S TCGA-AR-A24U 
      107.24       101.95        83.87        39.98        97.84        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LK 
       85.35        50.96        89.00        73.18        93.83        54.21 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WW TCGA-B6-A0X1 
      129.57        65.72       102.77       100.70        18.35       186.48 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 TCGA-BH-A0AU 
       58.88        43.59       139.17       170.17        68.12        24.53 
TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DE TCGA-BH-A0DP 
       59.84        51.68        24.85        48.69        31.17        15.65 
TCGA-BH-A0E9 TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       46.19        23.08        12.89        27.25        50.79        23.93 
TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1FM TCGA-BH-A5J0 TCGA-C8-A12O 
       26.66        51.39        51.16        45.63        23.51        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66        12.66        12.66         4.11         4.08        10.92 
TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A8HP 
       12.03         3.25         0.23        12.20         0.99        13.02 
TCGA-C8-A8HR TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JM 
       13.41        13.48        14.17        18.15        12.03        19.40 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR 
       17.79        27.58        18.15        15.22        19.92        15.85 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A27T TCGA-D8-A27W 
       16.54        15.32         9.93        13.48        13.08        12.26 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G 
       34.42        46.59        40.11        27.12        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 
       12.92        33.73        39.62        43.04         8.28        26.56 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA 
       12.00        36.56        12.59        28.27         6.12        32.09 
TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 
       32.09        21.27        34.13        23.51        17.06        27.22 
TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J6 TCGA-EW-A2FS 
        1.94        30.18         0.79        12.20        28.77        52.73 
TCGA-GI-A2C9 TCGA-GM-A2DL TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A5YM 
      109.87       115.69        72.03         2.60        11.57        15.32 
TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
       22.32        26.04        19.73         0.16        16.50        13.12 
TCGA-S3-AA17 
       13.94 

$`21Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5T-A9QA TCGA-A1-A0SB 
      129.14        40.14        11.44        48.56         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72       134.40        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        35.05        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       49.48        47.31        50.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        8.98         7.99        24.99         9.99        45.07        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        50.04        49.05        29.98        33.07         1.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A6 
       19.04        15.02         0.99        14.01        12.00        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        5.72         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70        33.04         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       16.31        14.83        22.19        14.99        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OR 
       18.67        13.58        12.26         1.68         0.03         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33        12.33         0.30         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03U 
        5.59        61.35        66.77        81.63        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       29.13        32.78        26.04        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       15.62        32.52         2.56        32.91        19.20        73.64 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        74.79        42.35        98.93        64.83        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       51.25        48.82        76.11        43.73        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       33.73       160.90        50.89        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24X 
       84.20         2.76       104.28        87.22        76.01        83.77 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        78.48        72.76        58.92       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
      143.38       149.59        12.13       220.90        50.70       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       172.96       162.05       140.48        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX 
      131.21       157.41        97.48       188.68        79.63        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KF 
      113.79       129.57       129.70        28.27        68.94       101.52 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW 
       73.51        85.35        74.99       103.63        71.15        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       48.36        56.94        56.98        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG 
       41.75        44.02        48.13        42.90        45.83        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        17.26         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX 
        5.85         2.50        13.61        36.85        51.32         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05         7.36        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28         8.94        18.64 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77        11.77        11.77        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
        0.39         3.16         2.24         1.87         1.12         1.05 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       12.33        11.34        11.28         0.16        10.42         2.30 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.36         0.43         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ 
        0.03         9.50         0.03         0.23        12.49        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        25.74        23.90        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.83        14.50        17.69        15.55        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.31         6.35        12.99        15.16        12.66        15.52 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18         8.02 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       12.10        43.00        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        18.51        25.41        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       21.63        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       27.42        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        12.85        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       36.82        13.48        13.12        39.55        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       25.84         9.86        11.90        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        21.21        40.24         1.12        34.65         6.58 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       34.59        35.64        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A249 
       22.75        41.03        12.89        20.71         0.69         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        29.72         0.76        26.07        18.41 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       15.72        12.33        23.84        14.70        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       15.39        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        72.10        85.15        86.96       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        62.43        11.84        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       25.05        17.06        14.70        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        14.73        14.07        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        17.36        14.07        28.21 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        16.93        16.80        15.39        13.84        15.35 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       14.96        13.84        17.03         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.16               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            186.48             234.28 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             24.53              24.56 
[1] "0.2 - 186.5 (24.5)" "0.0 - 234.3 (24.6)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED        11       13        0        0        52        46
  21Q LOSS WILD-TYPE      78       68        8        3       301       199
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         29         10          5        7
  21Q LOSS WILD-TYPE         1        121         19         58       13
                    vv
clus                 STAGE TIS STAGE X
  21Q LOSS MUTATED           1       3
  21Q LOSS WILD-TYPE         0      10
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                 13                 68
  STAGE IB                  0                  8
  STAGE II                  0                  3
  STAGE IIA                52                301
  STAGE IIB                46                199
  STAGE III                 1                  1
  STAGE IIIA               29                121
  STAGE IIIB               10                 19
  STAGE IIIC                5                 58
  STAGE IV                  7                 13
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of 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    40 107  19  11
  21Q LOSS WILD-TYPE 232 509 111  29
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               40                232
  T2              107                509
  T3               19                111
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    73  62  31   9
  21Q LOSS WILD-TYPE 428 288  86  66
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               73                428
  N1               62                288
  N2               31                 86
  N3                9                 66
[1] 4 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
  21Q LOSS MUTATED   147   8
  21Q LOSS WILD-TYPE 732  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    147    8
  21Q LOSS WILD-TYPE  732   13
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              147                732
  1                8                 13
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   178   0
  21Q LOSS WILD-TYPE 873  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    178    0
  21Q LOSS WILD-TYPE  873   11
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE              178                873
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q LOSS MUTATED                            0                           144
  21Q LOSS WILD-TYPE                          1                           619
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q LOSS MUTATED                               18                   2
  21Q LOSS WILD-TYPE                            174                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q LOSS MUTATED                       2                                7
  21Q LOSS WILD-TYPE                     2                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  21Q LOSS MUTATED                    1              4
  21Q LOSS WILD-TYPE                 16             44
D79V8, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 144                619
  INFILTRATING LOBULAR CARCINOMA                 18                174
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 23
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  4                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    51 127
  21Q LOSS WILD-TYPE 237 647
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     51  127
  21Q LOSS WILD-TYPE  237  647
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                51                237
  YES              127                647
[1] 2 2
[1] FALSE
D79V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0    17
  21Q LOSS WILD-TYPE                                1    43
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          34   109
  21Q LOSS WILD-TYPE                       136   627
D79V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                 43
  BLACK OR AFRICAN AMERICAN                      34                136
  WHITE                                         109                627
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 142
  21Q LOSS WILD-TYPE  34 716
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  142
  21Q LOSS WILD-TYPE   34  716
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 34
  NOT HISPANIC OR LATINO              142                716
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   400  65
  22Q LOSS WILD-TYPE 516  63
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               465                579 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                65                 63 
$`22Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14       131.67        42.81        14.37        14.27        13.68 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V 
       39.32        28.01       104.81        18.02        78.41        63.12 
TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       36.13        24.79        92.48        88.60       107.93        75.55 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EN 
        5.19        98.99       107.93        67.33        25.22       134.40 
TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0SU 
       80.28        35.05        34.29        31.82        61.94        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       27.12        50.43        49.84        20.52        18.90        20.75 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       25.28        18.21        50.47        21.90        21.67        23.77 
TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       17.36        20.25       107.70        42.44        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CE 
       29.98        50.37        38.37        21.30        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        30.61        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3J1 
       20.19        29.56        31.36        21.73        20.61        11.28 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        9.37         8.75        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08I 
        8.98         9.99        15.06        36.95        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A09B 
       37.05        31.00        33.01        40.01        12.00        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W 
        1.02        50.04         1.02         8.98        19.04         0.99 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G 
       13.02        21.04         0.99        27.02        17.03        10.85 
TCGA-AC-A2BK TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN 
       38.53        55.43        26.04        33.04        32.45        16.31 
TCGA-AC-A3QP TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
       22.19         1.55        17.42        18.67        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AJ TCGA-AN-A0AK 
        8.22        20.19         0.23         0.62         9.96         7.36 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.44         5.65         7.00         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L 
       12.33         0.33         0.33         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       66.77        95.70        21.40        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A12A TCGA-AO-A12E 
       21.53        50.70        72.00        26.24        90.58        57.30 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       82.62        61.87         0.53         2.56        32.91        19.20 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
        5.26        86.66        98.93        55.86       107.24        65.36 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AN 
       83.87       114.02        75.55        52.77        76.11        43.73 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24H 
       39.98        43.07        17.23        61.28        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       50.89        94.22        84.20         2.76        87.22        97.84 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
       50.96        83.77        79.00        89.00        73.18        58.92 
TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IG 
       93.83        54.21        39.39        16.04        20.45       146.50 
TCGA-B6-A0IH TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      112.37        84.59       110.14       140.88       211.56        68.45 
TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WW TCGA-B6-A0WX 
       81.17       172.96       162.05       102.77        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      113.79       139.17        68.12       103.63        71.15        24.53 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        46.95        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       56.98        51.68        37.22        25.71        21.70        44.05 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.69        45.57        49.94        49.05        48.13        42.90 
TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY 
       38.01         3.22         4.41         9.63        24.49        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HQ 
       10.78        23.08        41.00        52.96        26.50        36.85 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       12.89        27.25        23.93        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        8.81         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX 
        7.36        51.16       113.82        82.85        42.28        49.58 
TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FL 
       17.69        89.16        24.66       114.15        33.17        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ 
       45.63        72.07        83.31       130.16        10.52        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A138 
       23.51         9.63        11.77        12.66         1.87         4.08 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z 
       11.28        12.03        10.42         2.30         3.25         8.28 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
        9.53        12.20        13.02        19.46        11.90        20.88 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JD 
       14.17        13.48        21.14        14.17        18.71        18.15 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1X5 
       12.03        20.09        19.40        20.38        21.01        18.58 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XM 
       23.90        27.58        18.15        17.16        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.55        15.85         6.35        12.99        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27T TCGA-D8-A3Z5 
       14.24        14.14        14.43        16.41        13.08        33.37 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
       12.10        43.00        34.42        46.59        40.41        40.11 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V 
       28.87        44.68        38.24        38.60        33.30        34.26 
TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A159 TCGA-E2-A15A 
       32.02        18.51        25.41        23.24        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       11.05        13.02        19.56        14.99        60.53        53.03 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       32.35        17.10        37.41        33.73        33.70        28.44 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LK 
        3.88        22.19        20.98        39.62        28.90         8.75 
TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       16.93         8.28        34.92        26.56        34.29        12.85 
TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       34.82        36.82        12.00        13.12        36.56        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.77        35.24        25.84         9.86        34.95         2.56 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        32.09        32.09        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
        6.58        21.27        35.64        13.32        39.09        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       12.89        20.71         0.69        27.22         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       24.56        26.07        15.72        23.84        14.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 
       13.81        15.39        39.72        18.90        13.25        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 
       22.82        29.85        52.96        23.11        18.48         7.86 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DA 
       18.90         6.15        19.96        25.91        10.16       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A3NY TCGA-GM-A3XN 
       79.10        83.34        86.96       115.69        38.20        66.38 
TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 
       72.03         2.60        11.84        11.57        21.24         7.10 
TCGA-LL-A442 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LQ-A4E4 
       10.95        14.70        14.47        22.26        12.36        27.91 
TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66L 
       58.52        34.92        36.36        22.32        41.92        42.77 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       28.21        19.73        47.01        64.21        86.96         0.16 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UL-AAZ6 
        9.93        16.50        13.12        16.93        15.39        17.03 
TCGA-WT-AB44 TCGA-XX-A89A TCGA-Z7-A8R5 
       29.03        16.04       108.07 

$`22Q LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM 
       43.43        48.10        47.24        20.88        31.79         7.96 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       19.20        18.21       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX 
       55.43       136.73        99.12       114.81        75.25        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0EQ 
       34.55        33.76        61.58       101.72       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SW 
       74.40        72.00        24.72        63.29        99.19        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0YC 
       44.28        17.52        17.13         8.38        17.46        32.55 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        31.73        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        19.20        19.56        16.47        52.47 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        49.48        47.31        34.98         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0D9 TCGA-A7-A0DC 
       23.21        26.96        21.14        38.30        37.45        29.79 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A2KD 
       25.15        23.61        24.26        23.74        23.80        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       11.34        10.59        10.29        13.41        14.70        14.93 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O 
       12.10        10.72        11.05        10.29        10.42        13.02 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
        9.01        18.97         9.99        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       45.07        18.05        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       33.01         9.99        31.00         0.99       112.08        43.00 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09V 
       49.05        45.07        29.98        33.07        25.02        15.02 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       14.01        12.00        19.04        38.04         0.95         2.37 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK 
        5.72         1.48        99.35        40.57        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W5 
       50.70         0.92         2.27        14.83        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW 
       19.79        23.24        24.79        11.44        13.71        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        0.03         1.12         1.32         2.30         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         2.96         1.78         1.71         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         0.33         0.33         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R 
        0.30         5.33         5.59        61.35        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        32.78        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ 
       37.48        50.86        76.77        21.37        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      108.03        98.27        64.04        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       14.73        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        5.65        15.62        32.52       111.32        73.64        74.79 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK 
       42.35        64.83       101.95        85.97        61.84        51.25 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       48.82        43.56        37.81        76.21        63.62        62.14 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       96.89        78.51       104.28        76.01        53.36        85.35 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       78.48        72.76       143.21        20.25        62.86        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QQ 
       52.11        38.17        40.54        20.38        54.74        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
       50.70        65.72       176.98        18.77       126.12       110.93 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      189.01       234.28        78.02       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ 
      131.21       157.41        97.48       188.68        79.63       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AV 
      101.52        73.51       170.17        85.35        74.99        59.84 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       20.45        28.50        40.83        32.02        18.21        24.85 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW 
       61.68        35.67        48.69        27.19        53.95        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       41.75        44.02        45.83        31.17        23.44        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        48.23        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       67.86        47.41        16.27        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 
       46.19        32.58        31.00        24.43        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       35.51        24.56        20.38         5.85         2.50        13.61 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18N 
       51.32        50.79         5.59        24.95         2.01        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        55.63        37.55        66.05        51.39        69.93 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       91.99        12.00        55.69        25.81        31.53        97.48 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FR 
      120.62        74.73       122.89        36.92        63.35       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O 
       72.07        28.14        26.14        38.60        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FY 
        6.44        20.12       109.28         8.94         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        12.66         0.39 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        3.16         2.24         1.12         1.05         4.11        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.92        11.34         0.16         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        0.43         9.67         0.03         9.50         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        12.49        13.41        13.25        20.58        13.97 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       19.20        17.49        16.50        15.78        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JT 
       14.01        18.97        20.12        20.09        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XF 
       14.70        17.79        16.73        25.74        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XV 
       14.73        21.83        19.92        16.41        16.31        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       12.66        16.54        15.32        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       13.05         9.44        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        12.26        18.51        21.67        16.18         8.02 
TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S 
       27.52        37.51        28.44        47.15        40.96        33.17 
TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 
       43.33        31.96        28.60        27.12        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       23.87        14.79        17.29        19.40         9.04        20.58 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       17.06        14.07        53.62        33.01        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IK TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       38.30        32.78        22.65        11.08        54.18        27.42 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        40.47        18.87       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N6 
       43.04         5.52        15.72        30.61        32.88        13.48 
TCGA-E9-A1NC TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       39.55        11.90        28.27         6.12         3.02        21.21 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G 
       34.59        34.13        32.05        12.53        22.75        23.51 
TCGA-E9-A243 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       17.06         0.72        29.72         0.76        18.41        30.18 
TCGA-E9-A54X TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 
       12.33        14.40        12.20         8.48        18.21        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        25.94        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       29.82        30.08        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DD TCGA-GM-A2DF 
       23.51         7.40       109.87        59.57        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       72.10        85.15       106.06       101.62        85.35       110.50 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A74U 
       43.73        69.30        13.55        18.12        62.43        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        11.44        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       15.32        14.79         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        14.70        14.73        14.07        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        40.08        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66N TCGA-OL-A66O 
       20.38        26.70        23.47        65.62        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C TCGA-PL-A8LY TCGA-S3-AA0Z TCGA-S3-AA11 
       14.07        40.11         8.91         0.26        16.80        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G 
       15.35        14.96        13.84        13.94         3.81        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R6 
       52.96        15.35       107.05 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.16               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            216.76             234.28 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.05              23.87 
[1] "0.2 - 216.8 (25.1)" "0.0 - 234.3 (23.9)"
[1] "hr=" "1.4"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED        36       35        2        0       149       118
  22Q LOSS WILD-TYPE      53       46        6        3       204       127
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         67         12         35        7
  22Q LOSS WILD-TYPE         1         83         17         28       13
                    vv
clus                 STAGE TIS STAGE X
  22Q LOSS MUTATED           0       7
  22Q LOSS WILD-TYPE         1       6
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  36                 53
  STAGE IA                 35                 46
  STAGE IB                  2                  6
  STAGE II                  0                  3
  STAGE IIA               149                204
  STAGE IIB               118                127
  STAGE III                 1                  1
  STAGE IIIA               67                 83
  STAGE IIIB               12                 17
  STAGE IIIC               35                 28
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   7                  6
[1] 13  2
[1] TRUE
[1] "dimension of 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   113 287  51  17
  22Q LOSS WILD-TYPE 159 329  79  23
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1              113                159
  T2              287                329
  T3               51                 79
  T4               17                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED   213 158  53  41
  22Q LOSS WILD-TYPE 288 192  64  34
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0              213                288
  N1              158                192
  N2               53                 64
  N3               41                 34
[1] 4 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
  22Q LOSS MUTATED   396   8
  22Q LOSS WILD-TYPE 483  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    396    8
  22Q LOSS WILD-TYPE  483   13
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              396                483
  1                8                 13
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   464   6
  22Q LOSS WILD-TYPE 587   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    464    6
  22Q LOSS WILD-TYPE  587    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              464                587
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q LOSS MUTATED                            0                           349
  22Q LOSS WILD-TYPE                          1                           414
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q LOSS MUTATED                               84                   2
  22Q LOSS WILD-TYPE                            108                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q LOSS MUTATED                       2                               18
  22Q LOSS WILD-TYPE                     2                               12
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  22Q LOSS MUTATED                    1             13
  22Q LOSS WILD-TYPE                 16             35
D80V8, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 349                414
  INFILTRATING LOBULAR CARCINOMA                 84                108
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 12
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 13                 35
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   151 319
  22Q LOSS WILD-TYPE 137 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    151  319
  22Q LOSS WILD-TYPE  137  455
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               151                137
  YES              319                455
[1] 2 2
[1] FALSE
D80V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0    22
  22Q LOSS WILD-TYPE                                1    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          75   331
  22Q LOSS WILD-TYPE                        95   405
D80V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      75                 95
  WHITE                                         331                405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15 375
  22Q LOSS WILD-TYPE  23 483
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15  375
  22Q LOSS WILD-TYPE   23  483
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   15                 23
  NOT HISPANIC OR LATINO              375                483
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED   161  22
  XP LOSS WILD-TYPE 755 106
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              183               861 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22               106 
$`XP LOSS MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      129.14        47.24        31.79       121.94        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       24.79        75.55        75.25       107.93        67.33        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A4S3 
       25.22        80.28        27.12        17.52        83.01        21.90 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA 
       35.31        30.61        22.32        10.59        11.28        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06T 
       14.50        17.92        14.73         9.37         8.75        53.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08L TCGA-A8-A08O 
       29.03        26.01        15.06        36.95         9.99        31.00 
TCGA-A8-A099 TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM 
        9.99         1.02         0.99        17.03        38.04        99.35 
TCGA-AC-A7VB TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FD 
        8.22         2.96         7.36         0.16         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R 
        7.96         0.33         0.33         0.33         0.33        68.75 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA TCGA-AO-A0JE TCGA-AO-A0JI 
       32.78        21.40        52.18        21.53        76.77        50.24 
TCGA-AO-A124 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A54N 
      102.58        48.36        61.87        70.39        15.62         2.56 
TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       42.35        55.86       107.24       101.95       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A251 TCGA-AR-A254 
       75.55        33.73       104.28        87.22        78.48        72.76 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IQ 
       93.83        39.39        65.72       146.50        18.77       140.88 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A1KN 
       68.45        81.17       131.21        79.63        21.47       139.17 
TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0BW TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL 
       59.84        46.95        11.67        23.44        38.01        48.23 
TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0HA TCGA-BH-A0HW 
       47.41         9.63        24.43        10.78        52.96        51.32 
TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 TCGA-BH-A1FD 
       23.93        23.05       113.82        17.69        24.66        33.17 
TCGA-BH-A1FM TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 
       45.63        10.52        18.64        12.66        12.66         1.05 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W 
       10.92        11.34         0.16        10.42         0.30         0.23 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        9.53         9.50        12.49        13.41        19.46        11.90 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JM 
       19.20        17.49        16.50        18.71        18.97        19.40 
TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XO TCGA-D8-A27F TCGA-D8-A27H 
       21.01        23.90        27.58        15.55        16.04        13.05 
TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A158 
       10.09        13.08        28.60        27.12        21.04        14.79 
TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A1IE TCGA-E2-A1L7 TCGA-E2-A1L8 
       12.92        19.56        14.07        38.30        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NA 
       24.59       106.75        34.29        32.88        12.00        36.56 
TCGA-E9-A1NC TCGA-E9-A1R4 TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A3HO 
       39.55         6.12        21.27        23.51        27.22        26.07 
TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA 
       13.81        18.90        28.77        22.82        40.41        18.90 
TCGA-EW-A1PD TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LQ-A4E4 
       13.94        72.10         2.60        11.57        16.08        27.91 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66I TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       36.36        22.32        23.47        47.01        64.21         0.16 
TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
       16.93        14.96        16.04 

$`XP LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04W 
       18.21       104.81        18.02        78.41        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D2 
       88.60       107.93         5.19        98.99        56.81        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       61.58       101.72       134.40       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        49.48        47.31        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       26.96        21.14        38.30        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       21.73        20.61        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        13.74        21.17        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.29        10.42        13.02        13.02         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       45.07        18.05        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       33.01        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98        12.00         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
       50.04        49.05        45.07        29.98        33.07        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
        8.98        19.04        15.02        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04         0.99        27.02         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         5.72         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FK 
        9.96         6.51         0.33         0.33         5.65         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX 
        7.59         7.17         6.28         7.04         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J5 
       81.63        95.70        47.87        58.95        29.13        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       72.00        21.37        26.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        28.37        14.73        82.62 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       111.32        73.64         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 
       74.79        86.66        98.93        64.83        65.36        83.87 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       61.28        63.62        62.14       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
       96.89        78.51        84.20         2.76        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       73.18        58.92       143.21        20.25        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       66.15        52.11        38.17        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       220.90       129.57        50.70       112.37       176.98 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH 
      126.12        84.59       110.14       110.93       211.56       189.01 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       157.41        97.48       188.68        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       58.88        43.59       101.52        73.51       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       74.99        68.12       103.63        71.15        24.53        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        28.50        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       31.17        22.13        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        2.56        38.47        67.86        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       30.35        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 
       36.85        12.89        27.25        50.79         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        97.48       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       57.83       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
        8.94        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 
       11.77        12.66        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        2.24         1.87         1.12         4.11         4.08        12.33 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
       11.28        12.03         2.30         3.25         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        8.28         9.67         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        13.02        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        13.48        21.14        14.17        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        12.03        14.01        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.09        20.38        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        16.73        25.74        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        14.73        21.83        14.50        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.14        17.42        13.45        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       13.48         4.80         0.76        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18         8.02        12.10        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       31.96        18.51        25.41        23.24        19.43        23.87 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        17.42        19.40         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       13.02        17.06        14.99        60.53        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       33.01        32.35        28.50        16.47        17.10        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
       22.19        20.98        11.08        54.18        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90        18.87       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         8.28        30.61        34.92        26.56 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1ND 
       12.85        34.82        36.82        13.48        13.12        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        11.90        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         3.02         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       32.09        40.24         1.12        34.65         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13        32.05        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        41.03        12.89        20.71        17.06         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56         0.72        29.72         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41        30.18        15.72        12.33        23.84        14.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.21        13.25        16.57        15.68        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE 
       18.48        30.08         7.86        19.99         6.15        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        34.03        17.49        10.16        23.51         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U 
       72.03        13.55        18.12        62.43        11.84        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.79        22.26         2.63        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.70        12.36        14.73        14.07        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       28.87        24.72        20.38        26.70        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       42.77        26.04        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       40.11         8.91        86.96         0.26         9.93        16.50 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
       13.12        16.80        15.39        13.84        15.35        13.84 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35       108.07       107.05 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.16              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           146.50            234.28 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            23.51             24.72 
[1] "0.2 - 146.5 (23.5)" "0.0 - 234.3 (24.7)"
[1] "hr=" "1"  
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED        14       17        0        0        69        41
  XP LOSS WILD-TYPE      75       64        8        3       284       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           0         24          5          6        5
  XP LOSS WILD-TYPE         2        126         24         57       15
                   vv
clus                STAGE TIS STAGE X
  XP LOSS MUTATED           1       2
  XP LOSS WILD-TYPE         0      11
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                17                64
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               69               284
  STAGE IIB               41               204
  STAGE III                0                 2
  STAGE IIIA              24               126
  STAGE IIIB               5                24
  STAGE IIIC               6                57
  STAGE IV                 5                15
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    46 117  13   8
  XP LOSS WILD-TYPE 226 499 117  32
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              46               226
  T2             117               499
  T3              13               117
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP LOSS MUTATED    91  61  22  10
  XP LOSS WILD-TYPE 410 289  95  65
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              91               410
  N1              61               289
  N2              22                95
  N3              10                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   161   6
  XP LOSS WILD-TYPE 718  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    161    6
  XP LOSS WILD-TYPE  718   15
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             161               718
  1               6                15
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   183   3
  XP LOSS WILD-TYPE 868   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    183    3
  XP LOSS WILD-TYPE  868    8
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE             183               868
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP LOSS MUTATED                            0                           149
  XP LOSS WILD-TYPE                          1                           614
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP LOSS MUTATED                               19                   0
  XP LOSS WILD-TYPE                            173                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP LOSS MUTATED                       0                                6
  XP LOSS WILD-TYPE                     4                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XP LOSS MUTATED                    3              8
  XP LOSS WILD-TYPE                 14             40
D81V8, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                149               614
  INFILTRATING LOBULAR CARCINOMA                19               173
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    53 133
  XP LOSS WILD-TYPE 235 641
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     53  133
  XP LOSS WILD-TYPE  235  641
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               53               235
  YES             133               641
[1] 2 2
[1] FALSE
D81V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0    17
  XP LOSS WILD-TYPE                                1    43
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          38   114
  XP LOSS WILD-TYPE                       132   622
D81V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17                43
  BLACK OR AFRICAN AMERICAN                     38               132
  WHITE                                        114               622
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     6 152
  XP LOSS WILD-TYPE  32 706
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      6  152
  XP LOSS WILD-TYPE   32  706
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                32
  NOT HISPANIC OR LATINO             152               706
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   159  24
  XQ LOSS WILD-TYPE 757 104
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              183               861 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               24               104 
$`XQ LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04U 
      129.14       131.67        47.24        31.79       121.94        87.25 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
       75.55        75.25       107.93        67.33        34.55        25.22 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A3Y0 TCGA-A2-A4S3 
       80.28        27.12        17.52        83.01        38.37        21.90 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA 
       35.31        30.61        35.67        10.59        11.28        14.93 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06T TCGA-A8-A06U 
       17.92        14.73         9.37         8.75        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08I TCGA-A8-A08L 
       26.01        17.03        15.06        36.95        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A099 TCGA-A8-A09N TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM 
       31.00         9.99         1.02        17.03        38.04        99.35 
TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        8.22         1.12         0.23         9.96         7.36         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XL 
        0.33         0.33         6.44         7.96         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0JA TCGA-AO-A0JE 
        0.33         0.33        68.75        21.40        21.53        76.77 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A1KQ TCGA-AQ-A1H2 TCGA-AQ-A54N 
       50.24        62.04       102.58        61.87        15.62         2.56 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
        5.26        42.35        55.86       107.24        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A251 TCGA-AR-A255 
       85.97        75.55        33.73       160.90        78.48        58.92 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
       93.83        39.39        20.38        65.72       146.50        18.77 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0B0 
      140.88        68.45        81.17        21.47       139.17        46.95 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0GZ 
       53.69        49.94        23.44        38.01        47.41        10.78 
TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A1ES TCGA-BH-A1EY 
       52.96        12.89        51.32        23.93       113.82        17.69 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ 
       24.66        33.17        45.63       130.16        10.52        18.64 
TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL 
       12.66        12.66         1.05        10.92         0.16        10.42 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
        0.30         0.23        12.49        13.41        19.46        11.90 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JJ 
       19.20        17.49        16.50        18.71        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XJ 
       20.09        19.40        21.01        23.90        27.58        21.83 
TCGA-D8-A1XO TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A152 
       15.55        14.14        16.04        13.05        13.08        27.12 
TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15S 
       21.04        14.79        12.92         9.04        19.56        14.07 
TCGA-E2-A1IE TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 
       38.30        27.42        39.62       106.75        34.29        32.88 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 
       12.00        13.12        36.56        39.55        35.24         6.12 
TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 
       21.27        23.51        27.22        13.81        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PD TCGA-GM-A2DH TCGA-GM-A3XL 
       22.82        40.41        18.90        13.94        72.10        69.30 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5DA 
        2.60        11.57        16.08        12.36        27.91        58.62 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH 
       36.36        22.32        47.01        64.21         0.16        16.93 
TCGA-S3-AA14 TCGA-WT-AB44 TCGA-XX-A89A 
       14.96        29.03        16.04 

$`XQ LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        78.41        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
       92.48        88.60       107.93         5.19        98.99        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        61.58       101.72       134.40       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        50.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       26.96        21.14        38.30        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       33.11        29.79        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        13.74        14.50        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29        10.42        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        31.00         1.02        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       45.07        18.05        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       33.01        19.96        37.05        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        29.98        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04         0.99        27.02         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         5.72         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        0.03        20.19         1.32         2.30         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL 
        0.33         0.62         2.96         1.78         1.71         6.51 
TCGA-AN-A0AS TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         5.65         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        7.04         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        95.70        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       20.32        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       21.37        26.24        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       48.36        41.62        28.37        14.73        82.62        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       32.52        32.91        19.20       111.32        73.64        74.79 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AI 
       86.66        98.93        64.83        65.36       101.95        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        76.11        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14        50.89        94.22        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       84.20         2.76       104.28        87.22        97.84        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       73.18        72.76       143.21        20.25        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       66.15        52.11        38.17        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       20.45        10.59        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
      220.90       129.57        50.70       112.37       176.98       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93       211.56       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        74.99        68.12       103.63        71.15        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        20.45        25.55        28.50        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        35.67        48.69        27.19        53.95        45.57 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       45.83        31.17        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       15.65         3.22         2.56        38.47        67.86        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 
       32.58        24.49        31.00        24.43        30.35        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB 
       37.78        35.51        24.56        23.08        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX 
       20.38         5.85         2.50        13.61        36.85        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET 
        7.36        51.39        51.16        69.93        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        12.00        55.69        49.58        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        97.48       120.62       114.15        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O 
       28.14        26.14        38.60        83.31        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
        6.44        20.12       109.28         8.94        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66         0.39         3.16         2.24         1.87         1.12 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        4.11         4.08        12.33        11.34        11.28        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        2.30         3.25         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.53         0.03         9.50        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        13.02        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        13.48        21.14        14.17        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JN 
       18.90        12.03        12.03        14.01        20.12        20.38 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
        6.35        12.99        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I 
       15.52         9.93        14.24        17.42        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
        8.02        12.10        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        28.60        18.51 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A 
       25.41        23.24        19.43        23.87        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T 
       19.40        20.58        11.05        13.02        17.06        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        17.10        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 
        8.28        30.61        34.92        26.56        12.85        34.82 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       36.82        13.48        12.59        35.77        25.84         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        28.27        34.95         2.56         3.02         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        32.09        40.24         1.12        34.65 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        34.59        35.64        34.13        32.05        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       13.32        39.09        22.75        41.03        12.89        20.71 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06         0.69         1.94         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         0.76        26.07        18.41        30.18        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        23.84        14.70         0.79        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        25.94        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       52.96        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.43 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        11.44        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       14.70        14.47        14.79        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
        7.46        14.50        14.70        14.73        14.07        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
       19.73        40.11         8.91        86.96         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       16.50        13.12        16.80        15.39        13.84        15.35 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       13.84        13.94        17.03         3.81        11.41        52.96 
TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35       108.07       107.05 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.16              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           160.90            234.28 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            21.90             24.79 
[1] "0.2 - 160.9 (21.9)" "0.0 - 234.3 (24.8)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED        15       15        0        0        67        48
  XQ LOSS WILD-TYPE      74       66        8        3       286       197
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         22          4          6        5
  XQ LOSS WILD-TYPE         2        128         25         57       15
                   vv
clus                STAGE TIS STAGE X
  XQ LOSS MUTATED           1       2
  XQ LOSS WILD-TYPE         0      11
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 15                74
  STAGE IA                15                66
  STAGE IB                 0                 8
  STAGE II                 0                 3
  STAGE IIA               67               286
  STAGE IIB               48               197
  STAGE III                0                 2
  STAGE IIIA              22               128
  STAGE IIIB               4                25
  STAGE IIIC               6                57
  STAGE IV                 5                15
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of 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    41 121  15   8
  XQ LOSS WILD-TYPE 231 495 115  32
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              41               231
  T2             121               495
  T3              15               115
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    90  67  19   9
  XQ LOSS WILD-TYPE 411 283  98  66
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              90               411
  N1              67               283
  N2              19                98
  N3               9                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   159   6
  XQ LOSS WILD-TYPE 720  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    159    6
  XQ LOSS WILD-TYPE  720   15
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0             159               720
  1               6                15
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   184   3
  XQ LOSS WILD-TYPE 867   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    184    3
  XQ LOSS WILD-TYPE  867    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE             184               867
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ LOSS MUTATED                            0                           146
  XQ LOSS WILD-TYPE                          1                           617
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ LOSS MUTATED                               21                   1
  XQ LOSS WILD-TYPE                            171                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ LOSS MUTATED                       0                                8
  XQ LOSS WILD-TYPE                     4                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XQ LOSS MUTATED                    3              8
  XQ LOSS WILD-TYPE                 14             40
D82V8, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                146               617
  INFILTRATING LOBULAR CARCINOMA                21               171
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          0                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 8                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    52 135
  XQ LOSS WILD-TYPE 236 639
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     52  135
  XQ LOSS WILD-TYPE  236  639
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               52               236
  YES             135               639
[1] 2 2
[1] FALSE
D82V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0    15
  XQ LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          37   118
  XQ LOSS WILD-TYPE                       133   618
D82V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                45
  BLACK OR AFRICAN AMERICAN                     37               133
  WHITE                                        118               618
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     6 154
  XQ LOSS WILD-TYPE  32 704
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6  154
  XQ LOSS WILD-TYPE   32  704
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                32
  NOT HISPANIC OR LATINO             154               704
[1] 2 2
[1] FALSE
