[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/22506573/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/22531238/transformed.cor.cli.txt"

nPatients in clinical file=1097, in cluster file=1080, common to both=1079
[1]   82 1079
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              227               852 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              227               852 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              707               372 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              707               372 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               957 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               957 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73              1006 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73              1006 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              137               942 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              137               942 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              213               866 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              213               866 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75              1004 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75              1004 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               71              1008 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               71              1008 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              315               764 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              315               764 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              211               868 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              211               868 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              208               871 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              208               871 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              149               930 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              149               930 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              313               766 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              313               766 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              268               811 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              268               811 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              291               788 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              291               788 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              529               550 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              529               550 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              139               940 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              139               940 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              122               957 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              122               957 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               208                871 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               208                871 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               114                965 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               114                965 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               141                938 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               141                938 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                983 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                983 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               225                854 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               225                854 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               186                893 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               186                893 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                93                986 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                93                986 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                936 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                936 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                88                991 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                88                991 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               462                617 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               462                617 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               142                937 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               142                937 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               110                969 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               110                969 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               221                858 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               221                858 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               177                902 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               177                902 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               154                925 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               154                925 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               187                892 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               187                892 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               219                860 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               219                860 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               410                669 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               410                669 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               450                629 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               450                629 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               198                881 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               198                881 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                99                980 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                99                980 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              150               929 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              150               929 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              137               942 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              137               942 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              226               853 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              226               853 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               48              1031 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               48              1031 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              184               895 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              184               895 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              210               869 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              210               869 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              188               891 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              188               891 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              105               974 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              105               974 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              353               726 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              353               726 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              311               768 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              311               768 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              142               937 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              142               937 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              228               851 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              228               851 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              190               889 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              190               889 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              280               799 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              280               799 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              111               968 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              111               968 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              120               959 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              120               959 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              394               685 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              394               685 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               986 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               986 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              313               766 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              313               766 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              280               799 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              280               799 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               175                904 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               175                904 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               231                848 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               231                848 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               270                809 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               270                809 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               366                713 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               366                713 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               152                927 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               152                927 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               136                943 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               136                943 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               430                649 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               430                649 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               269                810 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               269                810 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               317                762 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               317                762 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               174                905 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               174                905 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               590                489 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               590                489 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               579                500 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               579                500 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               272                807 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               272                807 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               320                759 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               320                759 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               321                758 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               321                758 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               197                882 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               197                882 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               164                915 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               164                915 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                93                986 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                93                986 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                57               1022 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                57               1022 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               179                900 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               179                900 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               482                597 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               482                597 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              192               887 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              192               887 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              189               890 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              189               890 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 1079 columns.

[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=144,	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=717,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=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"
            2576    735    
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 1079 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"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=65, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
274 625 137  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
274 625 137  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
274 625 137  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
274 625 137  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
506 358 119  77 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
506 358 119  77 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
506 358 119  77 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
506 358 119  77 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, 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   199  26
  1P GAIN WILD-TYPE 718 122
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              225               840 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               122 
$`1P GAIN MUTATED`
TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A5ZX 
       19.20        36.13        31.36        24.26        21.73        11.05 
TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       49.05        45.07        19.79        14.53        19.33        13.71 
TCGA-AQ-A54O TCGA-AR-A2LR TCGA-E2-A1L8 TCGA-GM-A2DD TCGA-LD-A74U TCGA-LL-A5YP 
       32.91        57.27        73.64        75.02        13.22        14.79 
TCGA-3C-AALJ TCGA-A1-A0SF TCGA-A1-A0SM TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       48.46        48.10         7.96        73.84        87.25       101.98 
TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0SW 
       24.79        75.25        56.81        67.33        33.76        44.88 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B 
       49.48        18.61        19.33        31.73        20.25        42.44 
TCGA-A2-A3XS TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0DA TCGA-A7-A13D 
       33.93        50.37        50.83         7.30        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06Y 
       25.15        14.50        21.17        10.29         9.37        26.01 
TCGA-A8-A06Z TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08X 
        1.02         9.99        24.99        28.96         0.99        43.00 
TCGA-A8-A099 TCGA-A8-A09M TCGA-A8-A09R TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QJ 
        9.99        33.07         8.98        99.35        60.92        14.66 
TCGA-AC-A3QQ TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
       24.13        14.96        18.67        13.58         0.03         1.12 
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         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AO-A03R TCGA-AO-A0J2 
        0.33         7.59         7.04         0.33        68.75        32.78 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A128 TCGA-AO-A129 
       50.70        72.00        65.10        26.24       106.78       108.03 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AQ-A04L TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI 
       82.68        60.56       130.09        84.10       109.02       108.36 
TCGA-AR-A1AK TCGA-AR-A24K TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LQ 
      103.86        50.89       102.84        98.76        93.30        40.54 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RE TCGA-B6-A0RP 
      143.38       281.29        65.52       112.37       255.68       102.77 
TCGA-B6-A0RU TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AW 
      282.90       245.10        43.59        68.12        18.84        20.45 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       39.55        84.13        74.89        74.14        89.06        90.97 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E6 
       13.91        78.28         2.56        67.86        70.88         9.63 
TCGA-BH-A0EE TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0W3 TCGA-BH-A1F0 
       31.00        41.00        20.38         5.85        23.93        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FJ TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A203 
       31.53        97.48        63.35        72.07        55.50        38.60 
TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A135 TCGA-C8-A1HM 
       18.64        11.77        11.77        12.66        12.92        12.33 
TCGA-C8-A1HN TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Z 
       12.95        16.70         9.76        14.43        13.02        20.88 
TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JL 
       14.17        14.17        16.50        55.50        15.78        20.09 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XJ 
       13.32        18.58        27.58        18.15        12.39        21.83 
TCGA-D8-A1XK TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       14.50        43.04        16.54        10.09        13.08        12.26 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R 
       34.42        46.59        40.41        40.11        47.15        38.60 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 
       31.96        18.51        63.62        69.96        19.43        25.05 
TCGA-E2-A15D TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LI 
       17.29         9.04        76.57        33.70        60.36       102.61 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1RB 
       22.29        34.16        35.77        35.24        18.94        32.09 
TCGA-E9-A1RC TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A249 TCGA-E9-A3QA TCGA-E9-A3X8 
       40.24        46.59        34.45         7.13        30.18        30.44 
TCGA-E9-A54Y TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P8 
       23.84        16.57        25.94        22.82        41.13         7.86 
TCGA-EW-A1PB TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-GI-A2C9 
       19.99        25.91        17.52        16.77        24.99       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A7W5 
       59.57        70.85        72.10        62.47        11.57         7.10 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D7 
       32.75        17.06        14.47        16.08        15.68        58.52 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ 
       36.36        20.38        41.92        28.21         8.91         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-Z7-A8R6 
       18.48        21.07       107.05 

$`1P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A2-A25A 
       48.56        48.36        63.12        88.60        19.56       107.70 
TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 
       38.30        23.61        23.80        22.32        11.28        11.97 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S 
       53.06        29.03        19.99        15.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AO-A0JI 
       33.01        17.95         1.02        29.98        16.57        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         5.65         2.56        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       66.15        73.35        81.63        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O 
       89.16         9.70        10.42        21.14        14.79        50.79 
TCGA-E2-A1BC TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO 
       16.47        50.07        26.99        15.68        52.96        85.35 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       24.95        29.23        25.05        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI 
       13.94        11.41        52.96       108.07       133.05       131.67 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
       14.27        47.24        20.88        13.68        31.79        39.32 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        99.12       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 
       77.19         5.19        98.99       107.93        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       118.45        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-A0SX 
       24.72        63.29        99.19        54.64        27.12        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-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       50.47        21.90        21.67        48.46        23.77        23.47 
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-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
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-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       35.31        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       29.79        20.19        29.56        23.74        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        10.29        13.41        14.70        14.93        13.74 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX TCGA-A7-A6VY 
       17.92        14.73        12.10        10.72        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 
       13.02        13.02         1.02        17.98        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W 
       12.00        32.05        10.98         8.98         7.99         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-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-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
      112.08        40.01        30.97        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       12.00        50.04         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-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         5.72        22.26        73.05        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM 
       32.45         6.48        16.31        14.83        22.19        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP 
       11.44        17.42        12.26         1.68         8.22        20.19 
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-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.62         2.96         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         6.90         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         5.36         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        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        44.42        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27       113.62       108.72 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      102.31        98.27        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       97.08        61.87        82.62        11.51        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV 
       15.62        32.52       140.55        98.33         5.26        75.22 
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       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL 
       83.87       134.14       107.21       125.16       101.00        97.68 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       96.00        86.07        93.90        99.32        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
       97.84       105.27       105.30        50.96        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       99.62        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN 
       86.53        54.21        63.62        38.17        39.39        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       38.96        10.59        77.62        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70       146.50       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      165.76       129.07       140.88        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       263.28       162.05       140.28       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        74.99       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 
       59.84        25.55        63.09        81.44        39.16        70.22 
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        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C1 
       85.87        77.75        49.94        77.95        41.75        46.39 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DP 
       81.73        77.98        67.10        38.01        29.98        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        79.00        16.27         4.41        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        81.83        24.49        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA 
       15.16        63.39        53.26        24.56        23.08        52.96 
TCGA-BH-A0HB TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
       26.50         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79         5.59        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        32.91         4.90        35.93        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-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       17.69        25.08       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
      122.83        33.99        55.00        45.63        53.98        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       110.60        20.88        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        5.26        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.56        12.16        13.51        12.59        12.59        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.03        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 
       15.45        16.87         0.03        24.56        33.99        12.95 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        56.81        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE 
       13.97        13.48        19.20        17.49        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        53.00        14.01        18.97        20.09        20.12 
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-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       16.73        25.74        23.90        17.16        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        12.99        15.16        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        48.03        16.41        13.48        17.06         1.61 
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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       25.22        43.00        27.52        37.51        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        69.34        23.24        21.04        23.87 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       55.63        53.92        20.58        11.05        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       54.18        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG 
       36.82        36.20        36.56        39.55        41.62        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE 
        3.02        11.15        48.23        45.01         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        21.27        47.64        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
       20.12         0.69        38.99         1.94        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A5FK 
       29.72         9.47        38.07        32.91        23.90        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OX 
        8.48        18.21        18.90        13.25        28.77        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        40.41        39.78        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-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       17.49        23.51        15.22        31.30        33.21         7.40 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        79.10        83.34        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12         2.60        11.84 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       21.24        13.28        10.62        15.32        14.70        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        2.63         7.46        19.53        12.36        19.59        17.49 
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-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-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-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-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       18.81        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           282.90            275.87 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           28.210            28.205 
[1] "0.0 - 282.9 (28.2)" "0.0 - 275.9 (28.2)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED        16       15        1        2        75        60
  1P GAIN WILD-TYPE      73       68        5        4       277       193
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  1P GAIN MUTATED           0         28          9         14        1       2
  1P GAIN WILD-TYPE         2        127         18         51       19      11
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 16                73
  STAGE IA                15                68
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               75               277
  STAGE IIB               60               193
  STAGE III                0                 2
  STAGE IIIA              28               127
  STAGE IIIB               9                18
  STAGE IIIC              14                51
  STAGE IV                 1                19
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    42 144  26  14
  1P GAIN WILD-TYPE 232 481 111  26
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              42               232
  T2             144               481
  T3              26               111
  T4              14                26
[1] 4 2
[1] TRUE
[1] "dimension 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   116  74  21  15
  1P GAIN WILD-TYPE 390 284  98  62
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0             116               390
  N1              74               284
  N2              21                98
  N3              15                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   185   2
  1P GAIN WILD-TYPE 704  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    185    2
  1P GAIN WILD-TYPE  704   20
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0             185               704
  1               2                20
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   224   3
  1P GAIN WILD-TYPE 843   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    224    3
  1P GAIN WILD-TYPE  843    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE             224               843
  MALE                 3                 9
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    89 120
  1P GAIN WILD-TYPE 348 427
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     89  120
  1P GAIN WILD-TYPE  348  427
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               89               348
  YES             120               427
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P GAIN MUTATED                            0                           173
  1P GAIN WILD-TYPE                          1                           595
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P GAIN MUTATED                               24                   3
  1P GAIN WILD-TYPE                            177                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P GAIN MUTATED                       4                                8
  1P GAIN WILD-TYPE                     5                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  1P GAIN MUTATED                    2             13
  1P GAIN WILD-TYPE                 15             33
D1V9, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                173               595
  INFILTRATING LOBULAR CARCINOMA                24               177
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                13                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"
D1V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0    11
  1P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          47   154
  1P GAIN WILD-TYPE                       134   590
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     47               134
  WHITE                                        154               590
[1] 4 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     6 187
  1P GAIN WILD-TYPE  33 687
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6  187
  1P GAIN WILD-TYPE   33  687
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                33
  NOT HISPANIC OR LATINO             187               687
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   610  90
  1Q GAIN WILD-TYPE 307  58
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              700               365 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               90                58 
$`1Q GAIN MUTATED`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A25A 
       48.56        48.36        19.20        36.13        88.60       107.70 
TCGA-A7-A0CD TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J1 
       38.30        31.36        24.26        23.80        21.73        11.28 
TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A093 
       11.97        11.05        19.99        15.06        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
        1.02        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O 
       14.53        19.33        13.71        17.79         5.65        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO 
       19.20        98.33        66.15        57.27        73.35        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A1L8 
       32.58        21.44         9.70        10.42        21.14        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LD-A74U 
       50.07        26.99        15.68        52.96        75.02        13.22 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       25.05        14.79        40.08        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SE 
      108.07       131.67        48.46        47.61         9.96        43.43 
TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       48.10        47.24        20.88         7.96        39.32        18.21 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CK TCGA-A2-A0CM 
       78.41        73.84        87.25       101.98       136.73        24.79 
TCGA-A2-A0CO TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
      114.81        77.19        75.25        98.99        56.81        67.33 
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-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       79.76        35.05        31.82        63.29        99.19        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-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-A25B 
       31.73        23.77        23.47        22.45        20.25        42.44 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       17.19       105.34        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S2 TCGA-A7-A0CH 
       29.98        50.37        50.83         7.30        21.14        35.47 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       30.61        35.67        33.11        31.73        20.19        25.15 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SA 
       23.74        20.61        10.59        10.29        14.70        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-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q 
       10.72        10.29         9.37        10.42        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
       31.00        26.01         1.02        17.03        53.98        43.00 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       18.97        18.97         9.99         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G 
        9.99        45.07         0.99        38.01        28.96        19.96 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M 
       41.98        12.00         9.99         9.99        12.00        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        19.23 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       22.95        73.91         5.72        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        86.66        60.92        26.04        74.14        19.33 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QQ TCGA-AC-A3TM 
       14.66         6.48        16.31        14.83        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62Y 
       14.99        15.48        24.79        29.26        14.96        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
       18.67        13.58        12.26         1.68        20.19         1.12 
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-A0AS 
        1.71         9.96         7.36         7.46         0.16         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.90         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         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A03R 
       12.33         0.30         0.33         5.59        81.63        68.75 
TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       32.78        26.04        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.70        72.00        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       71.80       113.62       106.78       108.03       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       82.68        60.56        53.88        61.87        82.62        24.79 
TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
      130.09        32.52       140.55         5.26        84.10       109.02 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H 
       93.90        37.81        61.28        86.53        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q 
       50.89        94.22       120.33        99.78         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 
      112.77       102.84        50.96        98.76        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64        93.83       166.42        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 
       38.17        39.39        40.54        33.30        38.96        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE 
      143.38       281.29        11.90       275.87       129.57        65.52 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       233.62        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      255.68       212.25       234.28       263.28       162.05       102.77 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      100.70       282.90       188.68        79.46        18.35        21.01 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      206.86       129.70       245.10        58.55        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
       73.51       170.17         7.07        85.35        74.99        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       18.84       103.63        71.15        62.93        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA 
       63.09        81.44        39.55        70.22        84.13        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ 
       61.68        72.23        74.14        85.87        77.75        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG 
       41.75        46.39        89.06        90.97        81.73        67.10 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       29.98        13.91        78.28        15.65         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB 
       67.86        70.88        15.68         9.63        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HI 
       31.00        15.16        63.39        23.08        41.00        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-A0RX TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18L 
        5.59        23.93        32.91         4.90        90.84        26.66 
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-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        69.93        91.99        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FJ TCGA-BH-A1FL 
       49.58        25.81        31.53        97.48        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63        72.07        55.50        28.14        26.14        38.60 
TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
      130.16        36.79        20.12        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O 
        5.26        21.76         9.44        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       11.77        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM 
       13.51        12.92        12.33        11.28        12.03        12.33 
TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.95        12.36        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR 
        9.76        14.43        33.99        12.95        13.02        13.41 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 
       20.88        13.25        20.58        13.97        14.17        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        55.50        15.78        18.15        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-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       20.38        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        27.58        18.15        12.39        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       21.83        17.69        55.30        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        43.04        16.54        15.52         9.93 
TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27R 
       14.14        13.45        14.43        48.03        17.06        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.53        12.26        33.37        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       25.22        34.42        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        44.68        38.24        38.60 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       75.98        34.26        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D 
       69.96        23.24        19.43        25.05        23.34        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       20.71        18.21        12.92        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BD 
       11.05        51.39        76.57        53.62        32.35        37.25 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL 
       37.41        70.36        33.73        33.70        28.44         3.88 
TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A1LI 
       22.19        54.18        60.36        19.66       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A574 TCGA-E2-A9RU 
        8.75        34.55        43.56         8.28        38.76        17.69 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF 
       22.29        34.16        36.20        36.56        35.77        35.24 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       18.94         9.86        24.82        34.95         2.56         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF 
       48.23        45.01        32.09        40.24         1.12         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22A TCGA-E9-A22E 
       21.27        46.59        34.45        32.05        39.09        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       40.73        40.50        20.12        38.99         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
       12.33        29.72        38.07        30.18        30.44        23.84 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1J3 
       26.70        26.40        27.85        12.20        13.25        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 
       25.94        22.82        29.95        29.85        41.13        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR 
        7.86        19.99         6.15        10.52        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB 
       52.73        25.91        17.52        23.51        16.77        24.99 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
        7.40       109.87        59.57        83.34        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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       32.75        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A9Q3 
        2.63        16.08        15.68         7.46        19.53        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RV 
       27.91        22.39         2.10        58.52        58.62        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O 
       36.36        28.87        20.38        41.92        26.04        17.36 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LZ 
       28.21        19.73         8.91        64.21        86.96         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-UL-AAZ6 
       18.81        18.48        21.07        20.68        13.84        17.03 
TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
        3.81        29.03        15.35       107.05 

$`1Q GAIN WILD-TYPE`
TCGA-A2-A04V TCGA-A2-A1G4 TCGA-A7-A13G TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A06U 
       63.12        19.56        23.61        22.32        53.06        29.03 
TCGA-A8-A08S TCGA-A8-A091 TCGA-AO-A0JI TCGA-AQ-A54N TCGA-AR-A1AR TCGA-BH-A0B6 
       33.01        33.01        50.24         2.56        17.23        81.63 
TCGA-BH-A1F5 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-GM-A2DO TCGA-LL-A440 
       89.16        14.79        50.79        16.47        85.35        24.95 
TCGA-LL-A442 TCGA-LL-A740 TCGA-S3-AA12 TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A1-A0SB 
       29.23        14.50        18.87       133.05        11.44         8.52 
TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04N 
       14.37        14.27        13.68        31.79        28.01       143.15 
TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR 
       18.02       121.94        55.43        99.12        92.48       107.93 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
        5.19       107.93        34.55       118.45        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0T2 TCGA-A2-A0YE 
       34.29        61.94        24.72        54.64         8.38        18.21 
TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       50.47        17.36        60.72        19.20        16.47        52.47 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       18.15        10.59        32.75        56.28        47.31        35.93 
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-A0D9 TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A3IY TCGA-A7-A3RF 
       34.29        37.45        29.79        29.56        11.34        13.41 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A079 TCGA-A8-A07I TCGA-A8-A07J 
        8.75        13.02        17.98         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-A09D TCGA-A8-A09N TCGA-A8-A09T 
       37.05         9.99        31.00        50.04         1.02        19.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A3BB 
        0.99        38.04        90.71        87.12        33.04        32.45 
TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A7VB TCGA-AC-A7VC 
       22.19        23.24        16.80        11.44         8.22         0.03 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A04A TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.32         2.30         2.96         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        5.65         7.96         0.33         0.33         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U 
       80.28        61.35        66.77        95.70        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JC TCGA-AO-A0JE 
       44.42        21.40        52.18        37.48        50.86        76.77 
TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12E TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
      115.27       108.72        70.42        40.57        20.45        97.08 
TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW 
       11.51        26.93        15.62        98.33        75.22        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       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AX 
      134.14       107.21        86.07        99.32        94.29        86.43 
TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 
      118.59        97.84       105.27       105.30        98.66        99.62 
TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
       71.05        20.25        10.59        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RT 
      127.33        68.45        81.17        78.02       140.28        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KN 
      169.51        97.48       113.79        28.27        68.94       139.17 
TCGA-B6-A3ZX TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BP TCGA-BH-A0BR 
       37.87        59.84        39.16        51.68        75.48        76.60 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DZ 
       49.94        77.95        77.98        38.01         3.22        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
        4.41        14.30        44.81        63.32        30.35        10.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HY 
       53.26        24.56        52.96        26.50        51.32        50.79 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        44.81        23.05        35.93        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F8 
       72.56        37.74       113.82        82.85        17.69        25.08 
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       122.83        33.99 
TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42T TCGA-BH-A42U 
       53.98        83.31        57.83        36.82        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A8FZ TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X 
       20.88        18.87        11.77        12.66        12.66        12.66 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.59        12.46        12.49        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A27A 
        0.16        12.33        20.25        12.53        12.95        24.56 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JG 
       12.49        19.46        56.81        13.48        19.20        53.00 
TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XK 
       14.01        21.01        17.79        23.90        17.16        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       19.92        16.41        15.32        14.24        17.42        16.04 
TCGA-D8-A27H TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.05        16.41        13.48         1.61        18.51        21.67 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W 
       43.00        27.52        40.96        33.17        43.33        32.02 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15P 
       21.04        23.87        22.82        21.63        55.63        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE 
       56.94        14.07        87.22        33.01        28.50        77.65 
TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       59.18        60.99        11.08        24.59        75.81        28.90 
TCGA-E2-A1LL TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       43.04        30.61        34.92        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 
       36.82        39.55        41.62        25.84        28.27         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B 
       11.15        46.65        47.64        42.25        37.74        38.37 
TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54X 
       41.03         0.69         1.94         9.47        32.91        23.90 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.79        25.81        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-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        15.22        31.30        33.21       216.76        79.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A3XG TCGA-GM-A3XL 
       85.15        86.96       115.69       106.06        43.73        69.30 
TCGA-GM-A3XN TCGA-HN-A2NL TCGA-LD-A9QF TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 
       66.38         2.60        10.62        12.36        19.59        36.30 
TCGA-OL-A5D8 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       31.99        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       42.77        14.07        40.11        47.01         0.16         0.26 
TCGA-S3-AA10 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-XX-A89A 
       19.27        17.39        17.26        66.84        16.04 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           282.90            216.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            26.09             31.00 
[1] "0.0 - 282.9 (26.1)" "0.0 - 216.8 (31.0)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED        48       48        2        6       240       168
  1Q GAIN WILD-TYPE      41       35        4        0       112        85
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  1Q GAIN MUTATED           1         97         22         49       11       8
  1Q GAIN WILD-TYPE         1         58          5         16        9       5
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 48                41
  STAGE IA                48                35
  STAGE IB                 2                 4
  STAGE II                 6                 0
  STAGE IIA              240               112
  STAGE IIB              168                85
  STAGE III                1                 1
  STAGE IIIA              97                58
  STAGE IIIB              22                 5
  STAGE IIIC              49                16
  STAGE IV                11                 9
  STAGE X                  8                 5
[1] 12  2
[1] TRUE
[1] "dimension of 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   155 431  88  32
  1Q GAIN WILD-TYPE 119 194  49   8
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             155               119
  T2             431               194
  T3              88                49
  T4              32                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   331 236  72  56
  1Q GAIN WILD-TYPE 175 122  47  21
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             331               175
  N1             236               122
  N2              72                47
  N3              56                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   579  12
  1Q GAIN WILD-TYPE 310  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    579   12
  1Q GAIN WILD-TYPE  310   10
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             579               310
  1              12                10
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   700   7
  1Q GAIN WILD-TYPE 367   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    700    7
  1Q GAIN WILD-TYPE  367    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             700               367
  MALE                 7                 5
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   285 365
  1Q GAIN WILD-TYPE 152 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    285  365
  1Q GAIN WILD-TYPE  152  182
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              285               152
  YES             365               182
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q GAIN MUTATED                            1                           485
  1Q GAIN WILD-TYPE                          0                           283
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q GAIN MUTATED                              156                   4
  1Q GAIN WILD-TYPE                             45                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q GAIN MUTATED                       4                               18
  1Q GAIN WILD-TYPE                     5                               12
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  1Q GAIN MUTATED                    8             31
  1Q GAIN WILD-TYPE                  9             15
D2V9, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                485               283
  INFILTRATING LOBULAR CARCINOMA               156                45
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)              18                12
  MUCINOUS CARCINOMA                             8                 9
  OTHER, SPECIFY                                31                15
[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"
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                         111   501
  1Q GAIN WILD-TYPE                        70   243
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                    111                70
  WHITE                                        501               243
[1] 4 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    20 573
  1Q GAIN WILD-TYPE  19 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     20  573
  1Q GAIN WILD-TYPE   19  301
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  20                19
  NOT HISPANIC OR LATINO             573               301
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    98  21
  2P GAIN WILD-TYPE 819 127
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              119               946 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               127 
$`2P GAIN MUTATED`
TCGA-A7-A26I TCGA-E2-A158 TCGA-GM-A2DD TCGA-LL-A5YP TCGA-3C-AALI TCGA-3C-AALJ 
       21.73        14.79        75.02        14.79       131.67        48.46 
TCGA-A1-A0SO TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 
       28.01        56.81        67.33        50.43        17.13         8.38 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XZ TCGA-A2-A4S1 
       18.21        18.61        19.20        33.93        50.37        26.96 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A4SE TCGA-A7-A5ZV 
       30.61        35.67        31.73        20.19        21.17        12.10 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07U TCGA-A8-A08R 
        1.02        17.98        31.00        17.03        24.99         0.99 
TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A04C TCGA-AN-A0AM 
       12.00         5.72        17.42        13.58         1.78         0.16 
TCGA-AN-A0FX TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A12F 
        0.33        32.78        72.00       115.27        82.68        60.56 
TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A24Q 
       82.62        84.10        64.83        65.36        83.87       104.28 
TCGA-B6-A0I2 TCGA-B6-A0RE TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A3ZX TCGA-B6-A402 
      143.38       255.68       282.90       206.86        37.87        74.99 
TCGA-B6-A409 TCGA-BH-A0AW TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DL 
       18.84        20.45        61.51        41.75        46.39        78.28 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EV 
        9.63        81.83         7.36        51.16        69.93        12.00 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A203 TCGA-BH-A5IZ 
       31.53        97.48       114.15        45.63        38.60        18.64 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A1HK 
       11.77        12.66        12.66        12.16        13.51        12.03 
TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A143 
       12.95        16.70         9.76        13.02        20.88        14.17 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JK TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XU 
       19.20        14.17        20.12        15.22        19.92        12.99 
TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A159 TCGA-E2-A15A 
       13.48        10.09        40.11        40.96        25.05        23.34 
TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1RF TCGA-E9-A1RH 
       33.70        28.90         8.75        38.76         6.58        46.59 
TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FR 
       29.72         0.79         8.48        19.99         6.15        55.00 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-HN-A2NL TCGA-OL-A5RW TCGA-OL-A66I 
      109.87        79.10        70.85         2.60        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        19.27        17.03 

$`2P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       17.95         1.02        49.05        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT 
       19.79        14.53        19.33        13.71        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
        5.65         2.56        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A15O 
       21.44        89.16         9.70        10.42        21.14        50.79 
TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       16.47        73.64        50.07        26.99        15.68        52.96 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 
       85.35        13.22        24.95        29.23        25.05        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
      133.05        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ 
       43.43        48.10        14.27        47.24        20.88        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       31.79         7.96        39.32        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       78.41       121.94        73.84        87.25       101.98        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      136.73        99.12        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 
       77.19        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 
      118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       56.28        47.31        35.93        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        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-A13H 
       35.47        37.45        33.11        29.79        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        13.74        14.50        17.92        14.73 
TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       13.02        26.01         1.02        53.98         9.01        43.00 
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-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         8.98         7.99         9.99        45.07        18.05 
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-A08T 
       12.00        37.05         9.99        31.00        31.00       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        30.97        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       12.00        50.04        33.07         1.02        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-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 
       19.23        22.95        73.91        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       11.44        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-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-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         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         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
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        69.83        58.95        44.42 
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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       26.24        62.04        55.33        71.80       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G 
      106.78       108.03       102.31        98.27        70.42        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H 
       40.57        20.45        97.08        61.87        11.51        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26       109.02        75.22        98.93        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      133.22       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        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       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59        77.62       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      162.05       102.77       140.28       100.70        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 
      101.52        73.51       139.17       170.17         7.07        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
       68.12       103.63        71.15        62.93        59.84        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       63.09        81.44        39.55        39.16        70.22        84.13 
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        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 
       85.87        77.75        49.94        77.95        74.14        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       70.88        16.27         4.41        15.68        14.30        44.81 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        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-A1EO 
       30.28        55.63        37.55        66.05        51.39        91.99 
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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       25.81        25.08       120.62        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       33.99        63.35        55.00        72.07        53.98        55.50 
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        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
       36.79        20.12        10.52       110.60        20.88        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12X 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       48.53        12.56        12.59        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       15.45        16.87         0.03        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        13.97        13.48        17.49        16.50        55.50 
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        53.00        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-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-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.83        14.50        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31        16.64        15.16        43.04        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        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       17.06         1.61        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        12.66        25.22        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-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 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       18.51        63.62        69.96        23.24        19.43        21.04 
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        55.63        53.92         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        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 
       24.59        75.81       106.75       102.61        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        34.92        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        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        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
       40.24         1.12        46.65        21.27        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.72        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56        12.33         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       25.81        26.40        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
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-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-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       10.52        14.43        34.55        19.96        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
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-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       16.08        15.68         7.46        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       31.99        58.62        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-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       17.36        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       86.96         0.16         0.26        18.81        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ 
       20.68        13.84        17.39        17.26         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.16              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           282.90            281.29 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            23.34             28.82 
[1] "0.2 - 282.9 (23.3)" "0.0 - 281.3 (28.8)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         6        8        0        1        44        31
  2P GAIN WILD-TYPE      83       75        6        5       308       222
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  2P GAIN MUTATED           0         16          3          7        2       1
  2P GAIN WILD-TYPE         2        139         24         58       18      12
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  6                83
  STAGE IA                 8                75
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               44               308
  STAGE IIB               31               222
  STAGE III                0                 2
  STAGE IIIA              16               139
  STAGE IIIB               3                24
  STAGE IIIC               7                58
  STAGE IV                 2                18
  STAGE X                  1                12
[1] 12  2
[1] TRUE
[1] "dimension of 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    26  75  15   5
  2P GAIN WILD-TYPE 248 550 122  35
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              26               248
  T2              75               550
  T3              15               122
  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    55  41  16   8
  2P GAIN WILD-TYPE 451 317 103  69
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              55               451
  N1              41               317
  N2              16               103
  N3               8                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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   104   2
  2P GAIN WILD-TYPE 785  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    104    2
  2P GAIN WILD-TYPE  785   20
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             104               785
  1               2                20
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   122   0
  2P GAIN WILD-TYPE 945  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    122    0
  2P GAIN WILD-TYPE  945   12
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE             122               945
  MALE                 0                12
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    43  64
  2P GAIN WILD-TYPE 394 483
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     43   64
  2P GAIN WILD-TYPE  394  483
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               43               394
  YES              64               483
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P GAIN MUTATED                            1                           107
  2P GAIN WILD-TYPE                          0                           661
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P GAIN MUTATED                                5                   2
  2P GAIN WILD-TYPE                            196                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P GAIN MUTATED                       3                                1
  2P GAIN WILD-TYPE                     6                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  2P GAIN MUTATED                    0              3
  2P GAIN WILD-TYPE                 17             43
D3V9, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                107               661
  INFILTRATING LOBULAR CARCINOMA                 5               196
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 3                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"
D3V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1    11
  2P GAIN WILD-TYPE                                0    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          32    67
  2P GAIN WILD-TYPE                       149   677
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     32               149
  WHITE                                         67               677
[1] 4 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  39 770
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0  104
  2P GAIN WILD-TYPE   39  770
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO             104               770
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    62   9
  2Q GAIN WILD-TYPE 855 139
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               994 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               139 
$`2Q GAIN MUTATED`
TCGA-A7-A26I TCGA-LL-A5YP TCGA-3C-AALI TCGA-A1-A0SO TCGA-A2-A04W TCGA-A2-A0CX 
       21.73        14.79       131.67        28.01       101.98        56.81 
TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XZ TCGA-A2-A4S1 
       50.43        18.21        18.61        19.20        50.37        26.96 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A06R 
       30.61        35.67        31.73        21.17         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A07U TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AN-A04C 
       31.00        24.99        12.00         5.72        17.42         1.78 
TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A12F TCGA-AR-A24Q TCGA-B6-A0WZ TCGA-B6-A402 
      115.27        82.68        60.56       104.28       206.86        74.99 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E9 TCGA-BH-A18T 
       61.51        74.89        46.39        78.28        81.83         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-A130 TCGA-C8-A131 TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A8HP 
       12.66        12.16        13.51        12.95        16.70        13.02 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A10C TCGA-E2-A14P 
       19.20        14.17        12.99        13.48        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        38.76         0.79         8.48 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-LL-A5YN 
       19.99         6.15        55.00       109.87        79.10        14.70 
TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A66I TCGA-PL-A8LZ TCGA-S3-AA10 
       15.68        36.36        23.47         9.93        19.27 

$`2Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       17.95         1.02        49.05        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT 
       19.79        14.53        19.33        13.71        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
        5.65         2.56        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       21.44        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 
       50.79        16.47        73.64        50.07        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       25.05        14.50        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
       52.96       108.07       133.05        48.46        47.61        11.44 
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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       87.25        55.43       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        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       118.45        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-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-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-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       23.47        17.36        60.72        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       56.28        47.31        35.93        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        21.14        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F 
       35.47        37.45        33.11        29.79        20.19        25.15 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       13.41        14.70        14.93        13.74        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        8.75        13.02        13.02        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        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-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-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       30.97        41.98         9.99         9.99        12.00        50.04 
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        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV 
       24.79        29.26        16.80        14.96        11.44        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 
        7.46         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         6.90 
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 
        5.36         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        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        70.42        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        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       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.43        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      102.84       105.30        50.96        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.28       100.70        89.46       282.90       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.46        18.35        21.01       113.79       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.55        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       73.51       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       68.12        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       43.53        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        85.87        77.75        49.94        77.95        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        89.06        90.97        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       38.01        29.98        13.91        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30         9.63        44.81        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        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        32.91         4.90        35.93        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-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       12.00        55.69        49.58        17.69        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       25.08       120.62       114.15        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       33.99        63.35        55.00        45.63        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       55.50        28.14        26.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       18.64        23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        48.53        12.56        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
       20.25        12.53        12.36        15.45        16.87         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        9.76        24.56        14.43        33.99        12.95        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.97        14.17        13.48        17.49        16.50        55.50 
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        53.00        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-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        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        43.04        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        48.03        16.41        17.06         1.61        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        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        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        75.98        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        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C 
       69.96        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       75.81       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        34.92        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        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        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       38.37        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70        25.81        26.40        27.85 
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-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-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.52        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF 
       33.21         7.40        59.57       216.76        83.34        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-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        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       21.24         7.10        13.28        10.62        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z 
       15.32        14.47        22.26         2.63        16.08         7.46 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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-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-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        18.81        18.48        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.79              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           206.86            282.90 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            24.99             28.44 
[1] "0.8 - 206.9 (25.0)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         5        4        0        1        26        22
  2Q GAIN WILD-TYPE      84       79        6        5       326       231
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  2Q GAIN MUTATED           0          8          2          4        0       0
  2Q GAIN WILD-TYPE         2        147         25         61       20      13
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  5                84
  STAGE IA                 4                79
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               26               326
  STAGE IIB               22               231
  STAGE III                0                 2
  STAGE IIIA               8               147
  STAGE IIIB               2                25
  STAGE IIIC               4                61
  STAGE IV                 0                20
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    13  48  10   2
  2Q GAIN WILD-TYPE 261 577 127  38
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              13               261
  T2              48               577
  T3              10               127
  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    36  23   8   4
  2Q GAIN WILD-TYPE 470 335 111  73
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              36               470
  N1              23               335
  N2               8               111
  N3               4                73
[1] 4 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   0
  2Q GAIN WILD-TYPE 825  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     64    0
  2Q GAIN WILD-TYPE  825   22
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              64               825
  1               0                22
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    73   0
  2Q GAIN WILD-TYPE 994  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     73    0
  2Q GAIN WILD-TYPE  994   12
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              73               994
  MALE                 0                12
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    24  39
  2Q GAIN WILD-TYPE 413 508
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   39
  2Q GAIN WILD-TYPE  413  508
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               24               413
  YES              39               508
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q GAIN MUTATED                            0                            64
  2Q GAIN WILD-TYPE                          1                           704
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q GAIN MUTATED                                3                   0
  2Q GAIN WILD-TYPE                            198                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q GAIN MUTATED                       3                                0
  2Q GAIN WILD-TYPE                     6                               30
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  2Q GAIN MUTATED                    0              3
  2Q GAIN WILD-TYPE                 17             43
D4V9, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 64               704
  INFILTRATING LOBULAR CARCINOMA                 3               198
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                30
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 3                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"
D4V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     9
  2Q GAIN WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          18    39
  2Q GAIN WILD-TYPE                       163   705
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                51
  BLACK OR AFRICAN AMERICAN                     18               163
  WHITE                                         39               705
[1] 4 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  39 811
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   63
  2Q GAIN WILD-TYPE   39  811
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO              63               811
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED   114  23
  3P GAIN WILD-TYPE 803 125
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              137               928 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               125 
$`3P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09K 
       38.30        33.01        33.01        17.95        49.05        29.98 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-BH-A18H TCGA-E2-A1LG 
        2.56        32.91        66.15        81.63        21.44        50.07 
TCGA-LL-A5YP TCGA-A2-A04P TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SV 
       14.79        18.02        24.79        77.19        98.99        27.12 
TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A3XS 
       50.43         8.38        20.75        31.73        17.36        33.93 
TCGA-A2-A4RX TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A425 TCGA-A7-A4SD 
       24.39        35.67        33.11        25.15        14.70        14.50 
TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A08B 
       21.17        10.29        13.02         1.02         9.01        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A097 
       28.96        12.00        37.05         9.99        31.00        12.00 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H TCGA-AC-A2FM 
        9.99        12.00        25.02         8.98         5.72        26.04 
TCGA-AC-A2QJ TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A0AS TCGA-AN-A0FW 
       14.66        14.96        13.58         0.33         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03O TCGA-AO-A0J4 TCGA-AO-A0J7 
        0.33         0.33        12.33        81.63        52.18        20.32 
TCGA-AO-A128 TCGA-AO-A12D TCGA-AQ-A04H TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AS 
      106.78        82.68        24.79        84.10       108.36        37.81 
TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IA TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RP 
       50.89       105.30       275.87       140.88       255.68       102.77 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 
      100.70       282.90        79.46        43.59        85.35        68.12 
TCGA-BH-A0AU TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0DS 
       62.93        74.89        76.60        77.75        41.75         2.56 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N 
       81.83        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-A12L 
       51.39       114.15        26.14        38.60        23.51        11.93 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A1HI TCGA-C8-A27B TCGA-D8-A13Z 
       11.77        12.66        12.66        11.28        14.43        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 
       25.22        46.59        37.51        47.15        44.68        75.98 
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        76.57        33.73 
TCGA-E2-A1LI TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A54Y TCGA-E9-A5UP 
      102.61        32.09        40.24         6.58        23.84        26.40 
TCGA-EW-A1J6 TCGA-EW-A1P8 TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM 
       28.77         7.86        19.96        70.85        69.30        15.32 
TCGA-LL-A6FR TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-S3-A6ZF 
       16.08        36.36        20.38        28.21        18.81 

$`3P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09I 
       29.03        19.99        15.06        33.01         1.02        45.07 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
       16.57        19.79        14.53        19.33        13.71        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR 
       17.79         5.65        19.20        98.33        17.23        57.27 
TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       73.35        54.05        32.58        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A2P5 
       21.14        14.79        50.79        16.47        73.64        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       29.23        25.05        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ 
       11.41        52.96       108.07       133.05       131.67        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
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-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
        7.96        39.32        28.01        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
      121.94        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
       99.12       114.81        92.48       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       118.45        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-A0SY 
       24.72        63.29        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13        49.84        20.52        17.46        18.90 
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-A1FV 
       49.48        18.61        19.33        48.46        23.77        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.20        16.47        52.47 
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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        91.07        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.37        50.83         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-A13H 
       30.61        37.45        29.79        31.73        20.19        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.93        13.74        17.92        14.73        12.10        10.72 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X 
        9.37        10.42         8.75        13.02        17.98        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F 
       26.01         1.02        17.03        53.98        43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08O TCGA-A8-A08R 
       36.95        13.02         0.99        19.96        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
      112.08        43.00        40.01        30.97        41.98         9.99 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       50.04        33.07         1.02        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        19.23        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       60.92        87.12        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       11.44        17.42        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-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-A0AR TCGA-AN-A0AT 
        9.96         7.36         7.46         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-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.90         7.04         0.33         0.33         5.36         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-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 
       69.83        58.95        44.42        32.78        21.40        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       71.80       115.27       113.62       108.72       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L 
       97.08        61.87        82.62        11.51        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
       15.62        32.52       140.55        98.33         5.26       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        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-A1AJ 
      133.22        83.87       134.14       107.21       125.16       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
      112.77        97.84       105.27       102.84        50.96        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.66        89.00        99.62        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29        11.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.52       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       165.76       129.07        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       263.28       162.05       140.28        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      169.51        97.48       188.68        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
      101.52        73.51       139.17       170.17        37.87         7.07 
TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       74.99        18.84       103.63        71.15        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        63.09        81.44        39.55        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       85.87        49.94        77.95        74.14        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        78.28        15.65         3.22        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        31.00        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       26.50         5.85         2.50        13.61        36.85        12.89 
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        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        97.48        25.08       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       53.98        55.50        28.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       18.64         9.63         5.26        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        24.56        33.99        12.95        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        56.81        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       55.50        15.78        18.15        18.90        12.03        53.00 
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        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       43.04        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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48        17.06         1.61        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        12.66 
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        69.34        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        21.04        23.87        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        21.63        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       77.65        37.41        70.36        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LK 
       19.66        24.59        75.81        28.90       106.75         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       22.29        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH 
       48.23        45.01         1.12        46.65        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       38.37        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90        26.70         0.79        25.81        27.85        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-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-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-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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.52        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       33.21         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62       110.50        38.20        43.73        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        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       21.24         7.10        13.28        10.62        32.75        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        34.92 
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-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-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-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        18.48        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.33              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           282.90            281.29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            26.40             28.47 
[1] "0.3 - 282.9 (26.4)" "0.0 - 281.3 (28.5)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED        10        9        0        1        54        22
  3P GAIN WILD-TYPE      79       74        6        5       298       231
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  3P GAIN MUTATED           0         19          6          7        4       2
  3P GAIN WILD-TYPE         2        136         21         58       16      11
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 10                79
  STAGE IA                 9                74
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               54               298
  STAGE IIB               22               231
  STAGE III                0                 2
  STAGE IIIA              19               136
  STAGE IIIB               6                21
  STAGE IIIC               7                58
  STAGE IV                 4                16
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    31  85  11   9
  3P GAIN WILD-TYPE 243 540 126  31
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              31               243
  T2              85               540
  T3              11               126
  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    68  36  19  11
  3P GAIN WILD-TYPE 438 322 100  66
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              68               438
  N1              36               322
  N2              19               100
  N3              11                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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   124   4
  3P GAIN WILD-TYPE 765  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    124    4
  3P GAIN WILD-TYPE  765   18
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0             124               765
  1               4                18
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   136   1
  3P GAIN WILD-TYPE 931  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    136    1
  3P GAIN WILD-TYPE  931   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE             136               931
  MALE                 1                11
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    55  77
  3P GAIN WILD-TYPE 382 470
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     55   77
  3P GAIN WILD-TYPE  382  470
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               55               382
  YES              77               470
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P GAIN MUTATED                            0                           116
  3P GAIN WILD-TYPE                          1                           652
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P GAIN MUTATED                                7                   2
  3P GAIN WILD-TYPE                            194                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P GAIN MUTATED                       2                                4
  3P GAIN WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  3P GAIN MUTATED                    1              5
  3P GAIN WILD-TYPE                 16             41
D5V9, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                116               652
  INFILTRATING LOBULAR CARCINOMA                 7               194
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 5                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"
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                          28    82
  3P GAIN WILD-TYPE                       153   662
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                     28               153
  WHITE                                         82               662
[1] 4 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     5 102
  3P GAIN WILD-TYPE  34 772
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5  102
  3P GAIN WILD-TYPE   34  772
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             102               772
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   181  30
  3Q GAIN WILD-TYPE 736 118
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              211               854 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               118 
$`3Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26H TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E 
       38.30        23.80        33.01        33.01        17.95        49.05 
TCGA-A8-A09K TCGA-AC-A62X TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL TCGA-BH-A0B6 
       29.98        13.71         2.56        32.91        66.15        81.63 
TCGA-BH-A18H TCGA-E2-A1LG TCGA-LL-A5YP TCGA-A1-A0SI TCGA-A2-A04P TCGA-A2-A04U 
       21.44        50.07        14.79        20.88        18.02        87.25 
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0EY TCGA-A2-A0SV 
       24.79        77.19        98.99        67.33        63.29        27.12 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG 
       50.43        17.13         8.38        49.84        20.75        21.90 
TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A4RX 
       31.73        17.36        22.45        19.20        33.93        24.39 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A4SD 
       30.61        35.67        33.11        31.73        25.15        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q 
       21.17        14.73        10.29        10.42        13.02         1.02 
TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B 
        9.01        12.00        32.05        24.99         9.99        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A09A TCGA-A8-A09B 
       28.96        12.00         9.99        31.00         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ 
       33.07        25.02         8.98         5.72        26.04        14.66 
TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AJ 
       14.96        13.58         0.33         0.23         0.62         9.96 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        0.16         0.33         7.59         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A128 
       12.33        80.28        81.63        52.18        20.32       106.78 
TCGA-AO-A12D TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ 
       82.68        82.62        24.79        84.10       108.36       101.00 
TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24V TCGA-AR-A255 TCGA-AR-A256 
       37.81        50.89       120.33       105.30        71.05        93.83 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ 
       38.96       143.38       275.87       233.62        18.77       140.88 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A1KF 
      102.77       100.70       282.90        79.46        43.59       101.52 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT 
       85.35        68.12        62.93        74.89        76.60        77.75 
TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 
       41.75        78.28         2.56        81.83        24.49        23.08 
TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N TCGA-BH-A18Q 
       20.38        12.89        27.25        50.79        37.74        55.63 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A202 
       51.39        51.16        12.00       114.15        72.07        26.14 
TCGA-BH-A203 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12Q 
       38.60        18.64        23.51        11.93        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A1HI TCGA-C8-A26W TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
       12.66        11.28        12.53        14.43        12.95        13.02 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ 
       20.88        14.17        19.20        18.58        27.58        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y2 
       14.50        19.92        16.41        12.99        15.16        14.24 
TCGA-D8-A27R TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O 
       10.09        25.22        46.59        37.51        47.15        44.68 
TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ 
       18.51        19.43        25.05        20.71        18.21        76.57 
TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       77.65        33.73        33.70       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        34.16        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 
       46.59        23.84         0.79        26.40        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-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5S0 
       15.32        16.08        15.68        19.59        36.36        20.38 
TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z 
       28.21        86.96         9.93        18.81        21.07        20.68 
TCGA-UU-A93S 
        3.81 

$`3Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I 
       19.56       107.70        23.61        31.36        24.26        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09I TCGA-AC-A3W5 
       19.99        15.06        33.01         1.02        45.07        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       19.79        14.53        19.33        50.24        17.79         5.65 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO 
       19.20        98.33        17.23        57.27        73.35        54.05 
TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       32.58        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       50.79        16.47        73.64        26.99        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SO 
       47.24        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04W 
       18.21       143.15        78.41       121.94        73.84       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        99.12       114.81        92.48       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       118.45 
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-A1G6 
       48.46        23.77        23.47        60.72        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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 
       36.23        39.65        91.07        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       47.31        35.93        50.37        50.83         7.30        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-A0DC TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G 
       35.47        37.45        29.79        20.19        29.56        23.74 
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-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW 
       14.93        13.74        17.92        12.10        10.72         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        8.75        13.02        17.98        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98        43.00        18.97        18.97        14.01 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 
        9.99        10.98         8.98         7.99        45.07        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
       36.95        13.02         0.99        19.96        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 
        0.99       112.08        43.00        40.01        30.97        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V 
       12.00         9.99        50.04         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        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
       16.80        11.44        17.42        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-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.33         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        7.46         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY 
        7.00         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        5.36         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        0.33         5.33         5.59        61.35        66.77        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        69.83        58.95        44.42        32.78        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        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        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       115.27       113.62       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L 
       20.45        97.08        61.87        11.51        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
       15.62        32.52       140.55        98.33         5.26       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        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-A1AK 
      133.22        83.87       134.14       107.21       125.16       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AU 
       97.68        96.00        86.07        93.90        99.32        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      105.27       102.84        50.96        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       99.62        93.30        85.64       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       10.59        77.62       281.29        11.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.52       146.50       112.37       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      129.07       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       140.28        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        18.35        21.01       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI 
      129.70       245.10        28.27        68.94        58.55        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 
      139.17       170.17        37.87         7.07        74.99        18.84 
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        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       81.44        39.55        39.16        70.22        84.13        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        43.53        61.51        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        72.23        75.48        74.14        85.87        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.95        74.14        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP 
       77.98        67.10        38.01        29.98        13.91        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        79.00        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68        14.30         9.63        44.81        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        24.56 
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-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        51.32         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        32.91         4.90        35.93        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-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
        7.36        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       55.69        49.58        17.69        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.08       120.62        33.17        74.73       122.83        33.99 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       10.52       110.60        20.88         9.63         5.26        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
       21.76         9.44        11.77        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56        12.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.59        12.59        12.92        12.46        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34         0.16        12.03        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A8HQ 
       16.70         0.03         9.76        24.56        33.99        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        14.17        17.49        16.50        55.50        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        53.00        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-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XW 
       17.69        55.30        15.85        16.31        16.64        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        15.52         9.93        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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48        17.06         1.61        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 
       33.37        18.51        21.67        16.18        12.66        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        40.41        40.11        28.44        28.87 
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        75.98        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        69.34        63.62        69.96 
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-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       11.05        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IF 
       87.22        33.01        32.35        28.50        37.25        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       70.36        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       28.90         8.75        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       22.29        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        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        11.15        48.23        45.01 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        1.12        46.65        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO 
       32.91        30.18        30.44        23.90        26.70        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       13.25        16.57        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       41.13        39.78        23.11        18.48        30.08        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV 
       13.94        10.52        14.43        34.55        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
      216.76        83.34        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62       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-A66U 
       13.55        18.12        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN 
        7.10        13.28        10.62        32.75        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        22.26         2.63         7.46        19.53        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       31.99        58.62        34.92        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-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-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA11 
       64.21         0.16         0.26        18.48        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.39        17.26        17.03        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           282.90            281.29 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            25.05             29.03 
[1] "0.2 - 282.9 (25.1)" "0.0 - 281.3 (29.0)"
[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        80        42
  3Q GAIN WILD-TYPE      74       68        5        5       272       211
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  3Q GAIN MUTATED           0         29         10         11        5       1
  3Q GAIN WILD-TYPE         2        126         17         54       15      12
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                15                68
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               80               272
  STAGE IIB               42               211
  STAGE III                0                 2
  STAGE IIIA              29               126
  STAGE IIIB              10                17
  STAGE IIIC              11                54
  STAGE IV                 5                15
  STAGE X                  1                12
[1] 12  2
[1] TRUE
[1] "dimension of 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  22  13
  3Q GAIN WILD-TYPE 229 492 115  27
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              45               229
  T2             133               492
  T3              22               115
  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  59  26  15
  3Q GAIN WILD-TYPE 397 299  93  62
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             109               397
  N1              59               299
  N2              26                93
  N3              15                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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   185   5
  3Q GAIN WILD-TYPE 704  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    185    5
  3Q GAIN WILD-TYPE  704   17
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             185               704
  1               5                17
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   212   1
  3Q GAIN WILD-TYPE 855  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    212    1
  3Q GAIN WILD-TYPE  855   11
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE             212               855
  MALE                 1                11
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    85 116
  3Q GAIN WILD-TYPE 352 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     85  116
  3Q GAIN WILD-TYPE  352  431
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               85               352
  YES             116               431
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q GAIN MUTATED                            0                           181
  3Q GAIN WILD-TYPE                          1                           587
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q GAIN MUTATED                               10                   4
  3Q GAIN WILD-TYPE                            191                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q GAIN MUTATED                       4                                6
  3Q GAIN WILD-TYPE                     5                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  3Q GAIN MUTATED                    1              7
  3Q GAIN WILD-TYPE                 16             39
D6V9, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                181               587
  INFILTRATING LOBULAR CARCINOMA                10               191
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 7                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"
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                          47   129
  3Q GAIN WILD-TYPE                       134   615
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                     47               134
  WHITE                                        129               615
[1] 4 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     6 169
  3Q GAIN WILD-TYPE  33 705
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6  169
  3Q GAIN WILD-TYPE   33  705
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                33
  NOT HISPANIC OR LATINO             169               705
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    64  10
  4P GAIN WILD-TYPE 853 138
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               74               991 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               138 
$`4P GAIN MUTATED`
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AQ-A54O TCGA-AR-A2LL 
       33.01        33.01        29.98        16.57        32.91        66.15 
TCGA-Z7-A8R5 TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0ET TCGA-A2-A0YM 
      108.07        13.68        75.25         5.19        35.05        31.73 
TCGA-A2-A0YT TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06O 
       23.77        20.25        26.96        13.74        21.17        13.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08T 
       17.03         9.01        18.97         9.99        19.96       112.08 
TCGA-A8-A0A9 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0JD 
       27.02        33.04        14.66         1.78         0.33        72.00 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-B6-A0RG TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI 
       84.10        98.93        68.45        62.93        25.55        29.98 
TCGA-BH-A0DL TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1EW 
       78.28        27.25        26.66        37.74        69.93        55.69 
TCGA-BH-A1EX TCGA-BH-A1FM TCGA-BH-A202 TCGA-C8-A1HN TCGA-C8-A1HO TCGA-D8-A1J8 
       49.58        45.63        26.14        12.95        12.33        14.17 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XZ TCGA-D8-A27M 
       18.15        53.00        14.01        13.32        15.32        13.48 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A1LA 
       10.09        12.26        33.17        69.96        20.71        24.59 
TCGA-E2-A56Z TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A22D 
        8.28        36.20        11.15        40.24        46.65        41.03 
TCGA-E9-A247 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A6SA 
       38.99        26.40        29.82        52.73        25.91        16.77 
TCGA-LL-A5YN TCGA-S3-A6ZG 
       14.70        18.48 

$`4P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A093 
       53.06        29.03        19.99        15.06        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
        1.02        49.05        45.07        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       13.71        50.24        17.79         5.65         2.56        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       98.33        17.23        57.27        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 
       32.58        21.44        89.16         9.70        10.42        21.14 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 
       14.79        50.79        16.47        73.64        50.07        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       29.23        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ 
       13.94        11.41        52.96       133.05       131.67        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
      121.94        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS 
       99.12        24.79       114.81        92.48       107.93        77.19 
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       118.45 
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-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-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        23.47        17.36        60.72        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.20        16.47        52.47        42.44        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        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        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-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        14.70        14.93        14.50        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       53.98        43.00        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-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-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-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-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        9.99        12.00        50.04        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 
       19.23        22.95        73.91         5.72        22.26        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       26.04        74.14        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        29.26        16.80        14.96        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-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         7.46         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-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         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         5.36         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-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        44.42        32.78        21.40        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        65.10        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       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      102.31        98.27        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        20.45        97.08        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
       98.33         5.26       109.02        75.22        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       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       86.53        86.43        33.73       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27       102.84       105.30        50.96        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.66        89.00        99.62        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        74.99        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       71.15        59.84        20.45        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK 
       90.97        81.73        77.98        67.10        38.01        13.91 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       81.83        24.49        31.00        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        51.32        50.79         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        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       35.93        20.12        90.84        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        12.00        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       53.98        55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.88        18.64        23.51         9.63         5.26        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-A12Q 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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
       11.28         0.16        12.03        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 
       20.58        13.97        14.17        13.48        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       16.50        55.50        15.78        18.90        12.03        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-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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       43.04        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        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       16.41        17.06         1.61        13.08        12.53        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        12.66        25.22        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-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        75.98        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 
       69.34        18.51        63.62        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       23.87        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       60.36        19.66        75.81        28.90       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
        8.75        43.04        34.55        43.56        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       22.29        34.16        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        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        48.23        45.01 
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        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.72        40.73        40.50        20.12         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        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        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-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-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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       55.00        22.09        34.03        17.49        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        17.06        15.32 
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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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        18.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       21.07        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.33              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           112.08            282.90 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            26.53             28.44 
[1] "0.3 - 112.1 (26.5)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3        4        0        2        30        15
  4P GAIN WILD-TYPE      86       79        6        4       322       238
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  4P GAIN MUTATED           0         10          5          4        2       0
  4P GAIN WILD-TYPE         2        145         22         61       18      13
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 4                79
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               30               322
  STAGE IIB               15               238
  STAGE III                0                 2
  STAGE IIIA              10               145
  STAGE IIIB               5                22
  STAGE IIIC               4                61
  STAGE IV                 2                18
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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 261 580 126  34
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               261
  T2              45               580
  T3              11               126
  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 469 332 114  72
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              37               469
  N1              26               332
  N2               5               114
  N3               5                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    66   2
  4P GAIN WILD-TYPE 823  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     66    2
  4P GAIN WILD-TYPE  823   20
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              66               823
  1               2                20
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    73   2
  4P GAIN WILD-TYPE 994  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     73    2
  4P GAIN WILD-TYPE  994   10
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              73               994
  MALE                 2                10
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    27  40
  4P GAIN WILD-TYPE 410 507
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     27   40
  4P GAIN WILD-TYPE  410  507
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               27               410
  YES              40               507
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P GAIN MUTATED                            0                            58
  4P GAIN WILD-TYPE                          1                           710
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P GAIN MUTATED                                4                   1
  4P GAIN WILD-TYPE                            197                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P GAIN MUTATED                       3                                3
  4P GAIN WILD-TYPE                     6                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  4P GAIN MUTATED                    1              5
  4P GAIN WILD-TYPE                 16             41
D7V9, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 58               710
  INFILTRATING LOBULAR CARCINOMA                 4               197
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 5                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"
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                           9    51
  4P GAIN WILD-TYPE                       172   693
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                      9               172
  WHITE                                         51               693
[1] 4 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  36 816
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   58
  4P GAIN WILD-TYPE   36  816
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO              58               816
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    58  12
  4Q GAIN WILD-TYPE 859 136
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               70               995 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               136 
$`4Q GAIN MUTATED`
TCGA-A8-A06U TCGA-A8-A08S TCGA-A8-A091 TCGA-AC-A3W5 TCGA-AQ-A54O TCGA-AR-A2LL 
       29.03        33.01        33.01        16.57        32.91        66.15 
TCGA-E2-A15O TCGA-Z7-A8R5 TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0T3 
       50.79       108.07        13.68        75.25         5.19        49.84 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A8-A06O 
       31.73        23.77        20.25        26.96        13.74        13.02 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08T TCGA-A8-A0A9 
        9.01        18.97         9.99        19.96       112.08        27.02 
TCGA-AC-A2QJ TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0J3 TCGA-AR-A0TS TCGA-AR-A0TW 
       14.66         1.78         0.33        21.40        84.10        98.93 
TCGA-AR-A250 TCGA-B6-A0RG TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI 
       89.00        68.45        18.84        62.93        25.55        29.98 
TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FC 
       27.25        26.66        37.74        55.69        49.58       114.15 
TCGA-BH-A1FM TCGA-C8-A1HO TCGA-D8-A1J8 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT 
       45.63        12.33        14.17        53.00        14.01        13.32 
TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
       27.58        15.22        15.32        13.48        10.09        12.26 
TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A1LA TCGA-E9-A1R6 TCGA-E9-A1RC 
       33.17        69.96        20.71        24.59        11.15        40.24 
TCGA-E9-A1RE TCGA-E9-A247 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV 
       46.65        38.99        26.40        29.82        52.73        25.91 
TCGA-LL-A5YN TCGA-OL-A66I TCGA-S3-A6ZG TCGA-S3-AA10 
       14.70        23.47        18.48        19.27 

$`4Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A093 TCGA-A8-A09C 
       53.06        19.99        15.06        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       49.05        45.07        29.98        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       13.71        50.24        17.79         5.65         2.56        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       98.33        17.23        57.27        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 
       32.58        21.44        89.16         9.70        10.42        21.14 
TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 
       14.79        16.47        73.64        50.07        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       11.41        52.96       133.05       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV 
       24.79       114.81        92.48       107.93        77.19        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       118.45        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-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-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 
       48.46        23.47        17.36        60.72        22.45        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-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-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H 
       33.11        29.79        31.73        20.19        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       17.03        53.98        43.00        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-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-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       28.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 
        0.99        43.00        40.01        30.97        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
        9.99         9.99        12.00        50.04        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-A0AB 
       12.00        19.04        13.02        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       87.12        26.04        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        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-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.71         9.96         7.36         7.46         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-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.90         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         5.36         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-A0J4 
       68.75        69.83        58.95        44.42        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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03       102.31        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       60.56        53.88        40.57        20.45        97.08        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       82.62        11.51        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       32.52       140.55        98.33         5.26       109.02        75.22 
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       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        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       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        98.76        98.66        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
      255.68       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.28       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      169.51        97.48       188.68        79.46        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.55        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       37.87         7.07        85.35        74.99        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       71.15        59.84        20.45        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK 
       90.97        81.73        77.98        67.10        38.01        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        81.83        24.49        31.00        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        63.39        53.26        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-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        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        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P 
        4.90        35.93        20.12        90.84        72.56        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-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-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        97.48        25.08       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       110.60        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56        12.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.59        12.59        12.92        12.46        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       10.92        11.34        11.28         0.16        12.03        12.33 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 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-A1JP TCGA-D8-A1JS TCGA-D8-A1JU 
       20.09        19.40        20.38        21.01        12.20        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       18.58        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        17.16        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        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        43.04        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        48.03        16.41        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        38.60        75.98        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        69.34        18.51        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        60.36        19.66        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        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        48.23        45.01        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        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12         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        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 
       29.95        29.85        40.41        41.13        39.78        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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        17.06        15.32 
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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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        18.81        21.07 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       20.68        13.84        17.39        17.26        17.03         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        29.03        15.35        16.04       107.05 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.33              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           114.15            282.90 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            26.53             28.50 
[1] "0.3 - 114.2 (26.5)" "0.0 - 282.9 (28.5)"
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         4        5        1        0        28        13
  4Q GAIN WILD-TYPE      85       78        5        6       324       240
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  4Q GAIN MUTATED           0          9          5          4        2       0
  4Q GAIN WILD-TYPE         2        146         22         61       18      13
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  4                85
  STAGE IA                 5                78
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               28               324
  STAGE IIB               13               240
  STAGE III                0                 2
  STAGE IIIA               9               146
  STAGE IIIB               5                22
  STAGE IIIC               4                61
  STAGE IV                 2                18
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    18  38   9   6
  4Q GAIN WILD-TYPE 256 587 128  34
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              18               256
  T2              38               587
  T3               9               128
  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    33  26   5   5
  4Q GAIN WILD-TYPE 473 332 114  72
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              33               473
  N1              26               332
  N2               5               114
  N3               5                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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    63   2
  4Q GAIN WILD-TYPE 826  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     63    2
  4Q GAIN WILD-TYPE  826   20
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              63               826
  1               2                20
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    70   1
  4Q GAIN WILD-TYPE 997  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     70    1
  4Q GAIN WILD-TYPE  997   11
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              70               997
  MALE                 1                11
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    27  36
  4Q GAIN WILD-TYPE 410 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     27   36
  4Q GAIN WILD-TYPE  410  511
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               27               410
  YES              36               511
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q GAIN MUTATED                            0                            55
  4Q GAIN WILD-TYPE                          1                           713
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q GAIN MUTATED                                4                   2
  4Q GAIN WILD-TYPE                            197                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q GAIN MUTATED                       2                                2
  4Q GAIN WILD-TYPE                     7                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  4Q GAIN MUTATED                    1              5
  4Q GAIN WILD-TYPE                 16             41
D8V9, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 55               713
  INFILTRATING LOBULAR CARCINOMA                 4               197
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                28
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 5                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"
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                          11    47
  4Q GAIN WILD-TYPE                       170   697
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                     11               170
  WHITE                                         47               697
[1] 4 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  55
  4Q GAIN WILD-TYPE  36 819
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   55
  4Q GAIN WILD-TYPE   36  819
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO              55               819
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   266  46
  5P GAIN WILD-TYPE 651 102
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              312               753 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               46               102 
$`5P GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A093 
       19.20        38.30        22.32        29.03        33.01        17.95 
TCGA-A8-A09C TCGA-AC-A5EI TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL 
        1.02        14.53         5.65         2.56        32.91        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A18H TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A1LG 
       57.27        73.35        21.44         9.70        21.14        50.07 
TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI 
       26.99        14.79        11.41       108.07       133.05       131.67 
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0EO 
       13.68        39.32       101.98        56.81       134.40        80.28 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0SW 
       79.76        35.05        34.29        31.82        24.72        44.88 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW 
       18.90        20.75        18.21        21.90        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RX 
       60.72        20.25        42.44        29.98        50.37        24.39 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC 
       26.96        21.14        21.90        30.61        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       31.73        25.15        20.61        14.70        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       14.50        17.92        14.73        12.10        10.29         9.37 
TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Z TCGA-A8-A07G 
       10.42        13.02         1.02        17.98         1.02        18.97 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08G 
       24.99         9.99        45.07        13.02        38.01        19.96 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
       12.00        31.00         0.99        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
       12.00        25.02         8.98        14.01        12.00        13.02 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FE TCGA-AC-A2QJ TCGA-AC-A3HN 
       27.02        22.95        73.91        86.66        14.66        16.31 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03Y 
       14.96        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         5.36        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       102.31 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AR-A0TR 
       98.27        70.42        82.62        11.51        24.79         5.26 
TCGA-AR-A0TV TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24R 
       75.22       108.36       103.86        61.28        33.73       112.77 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A5QP 
      102.84       105.30        50.96        71.05        54.21        38.96 
TCGA-B6-A0I1 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KI 
       77.62       233.62       140.88        79.46       113.79        73.51 
TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AV 
       37.87        68.12        18.84       103.63        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA 
       20.45        63.09        39.55        70.22        84.13        37.22 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0C1 TCGA-BH-A0DI 
       43.53        21.70        74.89        75.48        46.39        29.98 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 
       15.65         2.56        24.49        31.00        63.32        23.08 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W5 TCGA-BH-A0W7 
       13.61        36.85        27.25        50.79        42.35        44.81 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN 
       90.84        26.66        72.56        37.74        51.39        69.93 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 
       91.99        42.28        12.00        55.69        31.53        97.48 
TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A2L8 TCGA-BH-A6R8 
       45.63        26.14        38.60        57.83        20.12         9.63 
TCGA-BH-A6R9 TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HI 
        5.26        11.77        12.66        12.16        12.92        11.28 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 
       12.03        12.33        14.43        13.97        14.17        17.49 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        53.00        14.01        20.09        20.12        20.09 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XL TCGA-D8-A1XS 
       13.32        17.79        27.58        18.15        19.92        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27H 
       12.99        43.04        16.54        15.52        14.24        13.05 
TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B 
       14.43        12.53        12.26        25.22        34.42        37.51 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14Y TCGA-E2-A14Z 
       44.68        40.96        33.17        75.98        69.34        18.51 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15L 
       69.96        23.24        21.04        20.71        18.21        20.58 
TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH 
       11.05        53.62        33.01        32.35        37.25        33.73 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LH 
       33.70        22.19        11.08        54.18        19.66       106.75 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NI TCGA-E9-A1R3 
       38.76        17.69        22.29        36.56         9.86         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC 
        6.12         3.02        11.15        48.23        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A243 TCGA-E9-A249 TCGA-E9-A295 
        1.12        21.27        46.59        20.12         7.13        12.33 
TCGA-E9-A3HO TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY 
       38.07        23.90        23.84         0.79        26.40         8.48 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD 
       16.57        28.77        29.82        23.11         6.15        13.94 
TCGA-EW-A423 TCGA-EW-A6SD TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A3NW TCGA-GM-A3XN 
       17.52        33.21        83.34        72.10       110.50        66.38 
TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LD-A66U TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A8F5 
       13.55        62.47        21.24        15.32         2.63        19.59 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DC 
       17.49        22.39        20.38        26.04         8.91        47.01 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UU-A93S TCGA-Z7-A8R6 
       86.96         0.16        18.48        21.07         3.81       107.05 

$`5P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        11.05        53.06        19.99        15.06 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01        33.01        49.05        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A7U7 
       19.79        19.33        13.71        50.24        17.79        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       98.33        17.23        81.63        54.05        32.58        89.16 
TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-EW-A1J5 
       10.42        14.79        50.79        16.47        73.64        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 
       25.05        14.50        40.08        18.87        13.94        52.96 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
       48.46        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
       43.43        48.10        14.27        47.24        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        73.84        87.25        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       24.79       114.81        92.48       107.93        77.19        75.25 
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-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       61.58        25.22       101.72       118.45        74.40        72.00 
TCGA-A2-A0EW TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       61.94        63.29        99.19        54.64        27.12        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-A1FV TCGA-A2-A1FZ 
       18.61        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       19.20        16.47        52.47        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        36.23        39.65        33.93        91.07        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       56.28        47.31        35.93        50.83         7.30        21.30 
TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       23.21        35.31        34.29        35.47        37.45        35.67 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       20.19        29.56        23.74        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A4SE TCGA-A7-A5ZW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06X 
       13.41        21.17        10.72         8.75        13.02        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
       26.01        17.03        53.98         9.01        43.00        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-A085 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08J 
        7.99        18.05        36.95         0.99        28.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00       112.08        43.00        40.01        30.97 
TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V 
        9.99        50.04        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 
       19.23         5.72        22.26        73.05        99.35        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       19.33        32.45         6.48        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       16.80        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        8.22         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.62         2.96         1.71         7.36         7.46         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         5.65         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XP 
        7.04         0.33         0.36         0.33         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N 
        0.33         0.33         0.33         5.33         5.59        66.77 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 
       95.70        68.75        69.83        58.95        44.42        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD 
       26.04        37.48        22.36        21.53        50.70        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       65.10        26.24        62.04       115.27       113.62       108.72 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      108.03        82.68        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       97.08        61.87        26.93       130.09        15.62        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
      140.55        98.33        84.10       109.02        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       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      107.21       125.16       101.00        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       93.90        99.32        37.81        94.29        86.53        86.43 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z 
        2.76       104.28        97.84       105.27        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        99.62        93.30        85.64        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        86.53        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       33.30        10.59       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK 
      129.57        50.70        65.52       146.50       112.37        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
      127.33        84.59       165.76       129.07       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.01       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.55        43.59       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C 
      139.17       170.17         7.07        85.35        74.99        71.15 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       25.55        81.44        39.16        51.68        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.51        61.68        72.23        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       77.75        49.94        77.95        74.14        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK 
       90.97        81.73        77.98        67.10        38.01        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       78.28         3.22        79.00        67.86        70.88        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        81.83 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        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-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA 
       12.89        51.32         5.59        23.93        24.95        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q 
       32.91         4.90        35.93        20.12        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05         7.36        51.16       113.82        82.85 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        17.69        25.81        25.08       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       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 
       72.07        53.98        55.50        28.14        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       36.82        36.79        10.52       110.60        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
       23.51        18.87        21.76         9.44        11.93        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-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       48.53        12.56        13.51        12.59        12.59        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HN 
       12.49        12.33        10.92        11.34         0.16        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
       16.87        16.70         0.03         9.76        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       20.88        13.25        20.58        14.17        13.48        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JI 
       16.50        55.50        15.78        18.15        12.03        18.97 
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-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-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.83        14.50        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       15.85        16.64        15.16        15.32         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        16.04        13.45        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       17.06         1.61        10.09        13.08        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       21.67        16.18        12.66        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q 
       40.41        40.11        28.44        28.87        47.15        38.24 
TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 
       38.60        43.33        34.26        32.02        31.96        63.62 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        23.87        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-A15P 
       21.63        12.92        55.63        53.92         9.04        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B6 
       56.94        14.07        51.39        76.57        87.22        28.50 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       77.65        37.41        70.36        28.44        59.18         3.88 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI 
       60.99        60.36        24.59        75.81        28.90       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       34.92        34.29        34.82        32.88        36.82        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.20        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A1RE 
       18.94        24.82        28.27        34.95        45.01        46.65 
TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
        0.69        38.99         1.94        24.56        29.72         9.47 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       32.91        30.18        30.44        26.70        25.81        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV 
       12.20        39.72        18.21        18.90        13.25        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-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE 
       18.48        30.08         7.86        18.90        19.99        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-EW-A6S9 TCGA-EW-A6SA 
       22.09        34.03        17.49        23.51        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       79.10        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PX 
      101.62        38.20        43.73        69.30        72.03        18.12 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
        2.60        11.84        11.57         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
       32.75        17.06        14.70        14.47        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       15.68         7.46        19.53        12.36        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        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        18.81        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ 
       19.27        13.84        17.39        17.26        17.03        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       29.03        15.35        16.04 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           233.62            282.90 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           23.805            30.180 
[1] "0.0 - 233.6 (23.8)" "0.0 - 282.9 (30.2)"
[1] "hr=" "1.5"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED        29       19        1        1       108        70
  5P GAIN WILD-TYPE      60       64        5        5       244       183
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  5P GAIN MUTATED           1         49          9         17        7       3
  5P GAIN WILD-TYPE         1        106         18         48       13      10
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 29                60
  STAGE IA                19                64
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA              108               244
  STAGE IIB               70               183
  STAGE III                1                 1
  STAGE IIIA              49               106
  STAGE IIIB               9                18
  STAGE IIIC              17                48
  STAGE IV                 7                13
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    73 182  46  13
  5P GAIN WILD-TYPE 201 443  91  27
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              73               201
  T2             182               443
  T3              46                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
  5P GAIN MUTATED   161  87  44  18
  5P GAIN WILD-TYPE 345 271  75  59
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             161               345
  N1              87               271
  N2              44                75
  N3              18                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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   271   7
  5P GAIN WILD-TYPE 618  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    271    7
  5P GAIN WILD-TYPE  618   15
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             271               618
  1               7                15
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   310   5
  5P GAIN WILD-TYPE 757   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    310    5
  5P GAIN WILD-TYPE  757    7
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             310               757
  MALE                 5                 7
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   119 166
  5P GAIN WILD-TYPE 318 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    119  166
  5P GAIN WILD-TYPE  318  381
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              119               318
  YES             166               381
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P GAIN MUTATED                            1                           228
  5P GAIN WILD-TYPE                          0                           540
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P GAIN MUTATED                               56                   2
  5P GAIN WILD-TYPE                            145                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P GAIN MUTATED                       7                                9
  5P GAIN WILD-TYPE                     2                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  5P GAIN MUTATED                    2             10
  5P GAIN WILD-TYPE                 15             36
D9V9, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                228               540
  INFILTRATING LOBULAR CARCINOMA                56               145
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          7                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                10                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"
D9V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    10
  5P GAIN WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          49   221
  5P GAIN WILD-TYPE                       132   523
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     49               132
  WHITE                                        221               523
[1] 4 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    11 253
  5P GAIN WILD-TYPE  28 621
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11  253
  5P GAIN WILD-TYPE   28  621
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             253               621
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   184  25
  5Q GAIN WILD-TYPE 733 123
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              209               856 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               25               123 
$`5Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A093 TCGA-A8-A09C TCGA-AC-A5EI TCGA-AQ-A0Y5 TCGA-AR-A2LL 
       38.30        17.95         1.02        14.53         5.65        66.15 
TCGA-AR-A5QM TCGA-BH-A18H TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A1LG TCGA-W8-A86G 
       73.35        21.44         9.70        21.14        50.07        11.41 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CX TCGA-A2-A0EN 
      108.07       133.05        13.68        39.32        56.81       134.40 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE 
       35.05        34.29        31.82        18.90        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A3XU TCGA-A2-A4RX 
       21.90        17.36        60.72        20.25        29.98        24.39 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F 
       26.96        21.14        30.61        33.11        29.79        25.15 
TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A8-A06O TCGA-A8-A06Q 
       20.61        14.70        13.74        14.50        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-A095 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09R 
       19.96         0.99        41.98        12.00        12.00         8.98 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G 
       14.01        12.00        13.02        27.02        22.95        73.91 
TCGA-AC-A2FE TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03Y 
       86.66        14.66        16.31         0.03        20.19         0.33 
TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0XO 
        9.96         0.16         0.33         7.00         0.33        12.33 
TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JC 
       80.28        81.63        32.78        20.32        53.03        50.86 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KS 
       76.77        71.80       102.31        98.27        70.42        11.51 
TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A24R TCGA-AR-A24V 
        5.26       108.36       103.86        61.28       112.77       105.30 
TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A5QP TCGA-B6-A0WV TCGA-B6-A0WY 
       50.96        71.05        54.21        38.96        79.46       113.79 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ 
       73.51        68.12        18.84       103.63        62.93        63.09 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 
       70.22        84.13        37.22        21.70        74.89        46.39 
TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 
       29.98        15.65         2.56        24.49        31.00        23.08 
TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L 
       36.85        27.25        42.35        44.81        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       72.56        37.74        51.39        69.93        91.99        42.28 
TCGA-BH-A1F6 TCGA-BH-A202 TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12P 
       97.48        26.14        20.12         9.63         5.26        11.77 
TCGA-C8-A135 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-D8-A1J8 TCGA-D8-A1JE 
       12.92        11.34        11.28        12.03        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        25.22        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        75.98        69.96        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        37.25        33.73        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 
       54.18        19.66       106.75         8.28        17.69        22.29 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC 
        9.86         2.56         6.12         3.02        11.15        40.24 
TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54X 
        1.12        21.27         7.13        12.33        29.72        23.90 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P5 
        0.79        26.40         8.48        16.57        28.77        23.11 
TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV 
        6.15        17.52        83.34       110.50        66.38        13.55 
TCGA-LD-A66U TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A66N 
       21.24         2.63        19.59        17.49        22.39        26.04 
TCGA-OL-A97C TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-Z7-A8R6 
        8.91        86.96        18.48        21.07       107.05 

$`5Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS 
       49.05        45.07        29.98        16.57        19.79        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       13.71        50.24        17.79         2.56        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       98.33        17.23        57.27        81.63        54.05        32.58 
TCGA-BH-A1F5 TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       89.16        10.42        14.79        50.79        16.47        73.64 
TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       26.99        15.68        52.96        75.02        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       24.95        29.23        25.05        14.79        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       18.87        13.94        52.96       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SO 
       14.27        47.24        20.88        31.79         7.96        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48       107.93        77.19        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-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       25.22       101.72        80.28       118.45        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-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-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        49.84        20.52        17.46        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 
       31.73        23.77        23.47        22.45        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       36.23        39.65        33.93        91.07        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       47.31        35.93        50.37        50.83         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-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY 
       35.67        31.73        20.19        29.56        23.74        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A4SF 
       10.59        10.29        13.41        14.93        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
        8.75        13.02        31.00        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        43.00        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-A082 
        9.99        10.98         8.98         7.99        24.99        18.05 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08J 
       36.95         0.99        38.01        28.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00        31.00       112.08        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
       30.97         9.99         9.99        50.04        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        19.23         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       73.05        99.35        40.57        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        74.14        33.04        19.33        32.45         6.48 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        29.26        16.80        14.96        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-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-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.78         1.71         7.36         7.46 
TCGA-AN-A0AR 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-A0FY 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT 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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       95.70        68.75        69.83        58.95        44.42        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-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 
       72.00        65.10        26.24        62.04        55.33       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F 
      113.62       108.72       106.78       108.03        82.68        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       53.88        40.57        20.45        97.08        61.87        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       98.33        84.10       109.02        75.22        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       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      107.21       125.16       101.00        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       93.90        99.32        37.81        94.29        86.53        86.43 
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       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       104.28        97.84       105.27       102.84 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       98.76        98.66        89.00        99.62        93.30        85.64 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       39.39        40.54        33.30        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.28       100.70        89.46       282.90       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        18.35        21.01       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN 
       28.27        68.94        58.55        43.59       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C 
      170.17        37.87         7.07        85.35        74.99        71.15 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        20.45        25.55        81.44        39.55        39.16 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM 
       51.68        32.02        18.21        43.53        61.51        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        77.95        74.14        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL 
       81.73        77.98        67.10        38.01        13.91        78.28 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        79.00        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI 
       15.68        14.30         9.63        44.81        81.83        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        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        32.91         4.90        35.93        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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       25.81        31.53        25.08       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       122.83        33.99        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        53.98        55.50        28.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U 
       57.83       130.16        36.82        36.79        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       20.88        18.64        23.51        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       13.51        12.59        12.59        12.46        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       10.92         0.16        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.76        24.56        14.43        33.99        12.95 
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        56.81        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        55.50        15.78        18.15        12.03 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       53.00        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        55.30        16.41        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       16.64        15.16        43.04        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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 
       13.48        17.06         1.61        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        12.66        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        69.34        18.51        63.62        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       23.87        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         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        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II 
       87.22        28.50        77.65        37.41        70.36        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA 
       28.44        59.18         3.88        60.99        60.36        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       75.81        28.90       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 
       43.56        30.61        34.92        38.76        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        34.16        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       41.62        35.77        35.24        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE 
       28.27        34.95        48.23        45.01        32.09        46.65 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       40.50        20.12         0.69        38.99         1.94        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        30.44        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       26.70        25.81        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 
      106.06       101.62        38.20        43.73        69.30        72.03 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 
       18.12         2.60        62.47        11.84        11.57         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        10.62        32.75        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       14.47        22.26        16.08        15.68         7.46        19.53 
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-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        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-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-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       64.21         0.16         0.26         9.93        18.81        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       19.27        13.84        17.39        17.26        17.03         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       66.84        29.03        15.35        16.04 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            134.4             282.9 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            22.19             30.13 
[1] "0.0 - 134.4 (22.2)" "0.0 - 282.9 (30.1)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED        19       16        1        1        67        48
  5Q GAIN WILD-TYPE      70       67        5        5       285       205
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  5Q GAIN MUTATED           1         35          5         14        1       2
  5Q GAIN WILD-TYPE         1        120         22         51       19      11
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                16                67
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               67               285
  STAGE IIB               48               205
  STAGE III                1                 1
  STAGE IIIA              35               120
  STAGE IIIB               5                22
  STAGE IIIC              14                51
  STAGE IV                 1                19
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    55 112  36   7
  5Q GAIN WILD-TYPE 219 513 101  33
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              55               219
  T2             112               513
  T3              36               101
  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  59  28  14
  5Q GAIN WILD-TYPE 399 299  91  63
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0             107               399
  N1              59               299
  N2              28                91
  N3              14                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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   179   1
  5Q GAIN WILD-TYPE 710  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    179    1
  5Q GAIN WILD-TYPE  710   21
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             179               710
  1               1                21
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   209   2
  5Q GAIN WILD-TYPE 858  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    209    2
  5Q GAIN WILD-TYPE  858   10
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE             209               858
  MALE                 2                10
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    77 114
  5Q GAIN WILD-TYPE 360 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     77  114
  5Q GAIN WILD-TYPE  360  433
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               77               360
  YES             114               433
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q GAIN MUTATED                            0                           140
  5Q GAIN WILD-TYPE                          1                           628
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q GAIN MUTATED                               47                   1
  5Q GAIN WILD-TYPE                            154                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q GAIN MUTATED                       6                                7
  5Q GAIN WILD-TYPE                     3                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  5Q GAIN MUTATED                    2              8
  5Q GAIN WILD-TYPE                 15             38
D10V9, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                140               628
  INFILTRATING LOBULAR CARCINOMA                47               154
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          6                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 8                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"
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   162
  5Q GAIN WILD-TYPE                       162   582
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               162
  WHITE                                        162               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"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7 169
  5Q GAIN WILD-TYPE  32 705
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7  169
  5Q GAIN WILD-TYPE   32  705
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             169               705
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED   174  33
  6P GAIN WILD-TYPE 743 115
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              207               858 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               33               115 
$`6P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26I TCGA-A8-A08S TCGA-A8-A09E TCGA-AC-A3W5 TCGA-AC-A62X 
       38.30        21.73        33.01        49.05        16.57        13.71 
TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-E2-A1LG 
        5.65        19.20        66.15        57.27        81.63        50.07 
TCGA-E2-A2P5 TCGA-LL-A740 TCGA-Z7-A8R5 TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO 
       26.99        14.50       108.07         9.96        31.79        28.01 
TCGA-A2-A04T TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET 
       73.84        55.43        24.79        33.76        79.76        35.05 
TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       31.82        63.29         8.38        18.21        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XV 
       31.73        23.77        60.72        17.19        33.93        32.75 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA 
       47.31        35.93        50.83        26.96        30.61        35.67 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       29.79        25.15        20.61        14.70        14.50        21.17 
TCGA-A7-A4SF TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F 
       17.92        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-A092 TCGA-A8-A09B TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QH 
       30.97        12.00        25.02        22.95        73.05        33.04 
TCGA-AC-A5XU TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AJ 
       14.96         0.03         1.12         0.33         0.23         9.96 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AO-A03L 
        0.16         7.00         0.36         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 
       66.77        81.63        55.33        71.80       115.27       108.03 
TCGA-AO-A12B TCGA-AO-A1KS TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U0 
       98.27        11.51         5.26        84.10        75.22        65.36 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
       61.28       160.90       104.28        98.66        89.00        71.05 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RU TCGA-B6-A0WY 
      143.38        11.90        84.59       165.76       282.90       113.79 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 
      245.10        43.59       101.52         7.07        74.99        68.12 
TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 
       18.84        71.15        59.84        20.45        25.55        39.55 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 
       37.22        61.51        74.89        77.75        74.14        46.39 
TCGA-BH-A0DH TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18Q 
       38.01        24.49        36.85        23.05        90.84        55.63 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC 
        7.36        69.93        91.99        12.00        31.53       114.15 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12X 
       38.60        57.83       130.16        18.64        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 
       12.16         0.16        12.33        12.36        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-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 
       10.09        12.53        31.96        18.51        63.62        25.05 
TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IN 
       11.05        14.07        53.62        33.70         3.88        22.19 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 
      106.75       102.61         8.28        34.92        38.76        36.20 
TCGA-E9-A1ND TCGA-E9-A1RF TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54Y 
       41.62         6.58        12.33        38.07        30.18        23.84 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       25.94        22.82        29.82        18.48        30.08         7.86 
TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-HN-A2NL 
       25.91        17.52        24.99       109.87        70.85         2.60 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 
        7.10        32.75        14.70        16.08        15.68        12.36 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DE TCGA-PL-A8LZ 
       58.62        36.36        20.38        23.47        86.96         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 
       18.81        20.68        19.27 

$`6P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI 
       45.07        29.98        19.79        14.53        19.33        50.24 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A5QM 
       17.79         2.56        32.91        98.33        17.23        73.35 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-EW-A1J5 
       21.14        14.79        50.79        16.47        73.64        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       25.05        14.79        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
       52.96       133.05       131.67        48.46        47.61        11.44 
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       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CK 
       18.02        78.41       121.94        87.25       101.98       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       99.12       114.81        92.48       107.93        77.19        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       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       74.40        72.00        34.29        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-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-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-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       48.46        23.47        17.36        22.45        20.25        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        52.47        42.44        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ 
       36.23        39.65        91.07        29.98        56.28        50.37 
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-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D 
       35.31        34.29        35.47        37.45        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       20.19        29.56        23.74        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.41        14.93        13.74        14.73        12.10        10.72 
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-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G 
        1.02        26.01         1.02         9.01        43.00        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-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G 
       45.07        18.05        36.95        13.02         0.99        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T 
       12.00        37.05         9.99        31.00        31.00       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        41.98        12.00         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        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        19.23        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        74.14        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       16.80        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         8.22        20.19         1.32         2.30         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         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         6.90         7.04         0.33 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         5.36        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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        69.83        58.95        44.42        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-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       65.10        26.24        62.04       113.62       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      102.31        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        61.87        82.62        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT 
      130.09        15.62        32.52       140.55        98.33       109.02 
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       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       94.29        86.53        86.43        33.73        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
      105.27       102.84       105.30        50.96        98.76        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       38.96        10.59        77.62       281.29       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      127.33       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.28       100.70        89.46       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       79.46        18.35        21.01       206.86       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.55        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
       85.35       103.63        62.93        63.09        81.44        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        51.68        32.02        18.21        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       85.87        49.94        77.95        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       81.73        77.98        67.10        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       81.83        31.00        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        32.91         4.90        35.93        20.12 
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-A18U TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.39        51.16       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       49.58        17.69        25.81        97.48        25.08       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.83        33.99        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        53.98        55.50        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.59        12.59        12.92        12.46        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO 
       10.92        11.34        11.28        12.03        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.76        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       13.02        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        13.48        19.20        17.49        16.50        55.50 
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        53.00        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        55.30        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        15.16        43.04        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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
       13.48        17.06         1.61        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        12.66        25.22        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        75.98        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       69.34        69.96        23.24        19.43        21.04        23.87 
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-A15P 
       12.92        55.63        53.92         9.04        20.58        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        51.39        76.57        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       28.44        59.18        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL 
       19.66        24.59        75.81        28.90         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       34.55        43.56        30.61        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        22.29        34.16        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       24.56        29.72         9.47        32.91        30.44        23.90 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        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-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       28.77        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       23.11        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-A2FW 
       14.43        34.55        19.96        55.00        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       34.03        17.49        23.51        15.22        16.77        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21         7.40        59.57       216.76        79.10        83.34 
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-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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP 
       13.28        10.62        17.06        15.32        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        2.63         7.46        19.53        19.59        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RV 
       22.39         2.10        36.30        58.52        31.99        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       28.87        24.72        22.32        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-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-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       18.48        21.07        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        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 
           282.90            281.29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            25.94             28.44 
[1] "0.0 - 282.9 (25.9)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED        15       10        0        1        78        52
  6P GAIN WILD-TYPE      74       73        6        5       274       201
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  6P GAIN MUTATED           0         29          8         10        3       1
  6P GAIN WILD-TYPE         2        126         19         55       17      12
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                10                73
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               78               274
  STAGE IIB               52               201
  STAGE III                0                 2
  STAGE IIIA              29               126
  STAGE IIIB               8                19
  STAGE IIIC              10                55
  STAGE IV                 3                17
  STAGE X                  1                12
[1] 12  2
[1] TRUE
[1] "dimension of 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    39 135  26   8
  6P GAIN WILD-TYPE 235 490 111  32
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              39               235
  T2             135               490
  T3              26               111
  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 GAIN MUTATED   104  61  27  11
  6P GAIN WILD-TYPE 402 297  92  66
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0             104               402
  N1              61               297
  N2              27                92
  N3              11                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   171   4
  6P GAIN WILD-TYPE 718  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    171    4
  6P GAIN WILD-TYPE  718   18
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             171               718
  1               4                18
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   207   1
  6P GAIN WILD-TYPE 860  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    207    1
  6P GAIN WILD-TYPE  860   11
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE             207               860
  MALE                 1                11
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    73 117
  6P GAIN WILD-TYPE 364 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     73  117
  6P GAIN WILD-TYPE  364  430
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               73               364
  YES             117               430
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P GAIN MUTATED                            0                           165
  6P GAIN WILD-TYPE                          1                           603
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P GAIN MUTATED                               21                   5
  6P GAIN WILD-TYPE                            180                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P GAIN MUTATED                       4                                4
  6P GAIN WILD-TYPE                     5                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  6P GAIN MUTATED                    1              7
  6P GAIN WILD-TYPE                 16             39
D11V9, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                165               603
  INFILTRATING LOBULAR CARCINOMA                21               180
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 7                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"
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                          50   131
  6P GAIN WILD-TYPE                       131   613
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                     50               131
  WHITE                                        131               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"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9 163
  6P GAIN WILD-TYPE  30 711
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  163
  6P GAIN WILD-TYPE   30  711
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             163               711
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED   124  24
  6Q GAIN WILD-TYPE 793 124
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              148               917 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               24               124 
$`6Q GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A8-A08S TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A7U7 
       19.20        38.30        33.01        13.71         5.65        19.20 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-E2-A2P5 TCGA-Z7-A8R5 TCGA-A1-A0SJ 
       66.15        57.27        81.63        26.99       108.07        13.68 
TCGA-A1-A0SK TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY 
       31.79        55.43        24.79        33.76        79.76        63.29 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FX TCGA-A2-A1G1 
        8.38        18.21        21.90        18.61        60.72        19.20 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC 
       47.31        35.93        26.96        30.61        35.67        29.79 
TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A8-A06R TCGA-A8-A06X 
       14.70        14.50        21.17        17.92        17.98        31.00 
TCGA-A8-A075 TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R 
       17.03        18.97         8.98        38.01        28.96         0.99 
TCGA-A8-A09B TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A5XU TCGA-AC-A7VC 
       12.00        25.02        22.95        33.04        14.96         0.03 
TCGA-AN-A03Y TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AO-A03O TCGA-AO-A124 
        0.33         0.16         7.00         0.33        81.63       115.27 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      108.03        98.27        11.51        84.10       109.02        75.22 
TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24Z 
       65.36       108.36        61.28       160.90       104.28        98.66 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IO TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 
      143.38        11.90       165.76         7.07        74.99        18.84 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL 
       59.84        25.55        39.55        37.22        61.51        74.89 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18Q 
       77.75        74.14        46.39        24.49        36.85        55.63 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       91.99        12.00        31.53        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ 
       18.64        23.51        11.93        12.66        12.16         0.16 
TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 
       12.33        12.36        20.88        13.97        14.17        14.17 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.09        20.09        21.01        18.58        21.83        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27V 
       16.41        16.54        15.32        14.14        16.04        12.53 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1B0 
       31.96        18.51        63.62        25.05        11.05        53.62 
TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1NF 
       33.70       106.75        34.92        38.76        36.20        35.24 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       30.18        23.84        25.94        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-HN-A2NL 
        7.86        17.52       109.87        70.85        72.10         2.60 
TCGA-LD-A7W5 TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 TCGA-OL-A5DA 
        7.10        14.70        16.08        15.68        12.36        58.62 
TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
       86.96         9.93        20.68        19.27 

$`6Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       49.05        45.07        29.98        16.57        19.79        14.53 
TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM 
       19.33        50.24        17.79         2.56        32.91        98.33 
TCGA-AR-A1AR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       17.23        73.35        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       73.64        50.07        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU 
       40.08        18.87        13.94        11.41        52.96       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        48.46        47.61        11.44         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-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        39.32        28.01        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CK 
       78.41       121.94        73.84        87.25       101.98       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       99.12       114.81        92.48       107.93        77.19        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       118.45 
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-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       17.36        22.45        20.25        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       33.93        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         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-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB 
       11.34        10.59        10.29        13.41        14.93        13.74 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06Y TCGA-A8-A06Z 
        8.75        13.02        13.02         1.02        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        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-A08G 
       45.07        18.05        36.95        13.02         0.99        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T 
       12.00        37.05         9.99        31.00        31.00       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-A09A TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
        9.99        50.04        33.07         1.02         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        19.23 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79        29.26        16.80        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ 
       13.58        12.26         1.68         8.22        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         7.46 
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-A0FW 
        7.59         7.17         6.90         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         5.36         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-A03P TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        66.77        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        44.42        32.78        21.40        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        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       55.33        71.80       113.62       108.72       106.78       102.31 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       82.68        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       97.08        61.87        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TW 
       15.62        32.52       140.55        98.33         5.26        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       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       125.16       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       86.07        93.90        99.32        37.81        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       112.77        97.84       105.27       102.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
      105.30        50.96        98.76        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       38.96        10.59        77.62       281.29       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      127.33        84.59       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
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        62.93        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       63.09        81.44        39.16        70.22        84.13        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        43.53        21.70        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        89.06        90.97        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        79.00        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE 
       15.68        14.30         9.63        44.81        81.83        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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        32.91         4.90        35.93        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-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        69.93       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       42.28        55.69        49.58        17.69        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       25.08       120.62       114.15        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       33.99        63.35        55.00        45.63        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       55.50        28.14        26.14        83.31        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 
       20.12        10.52       110.60        20.88         9.63         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
       12.49        12.33        10.92        11.34        11.28        12.03 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        12.33        20.25        12.53        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 
       56.81        13.25        20.58        13.48        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       53.00        14.01        18.97        20.12        19.40        20.38 
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-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-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.73        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        12.99        15.16        43.04        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       14.24        17.42        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        10.09        13.08 
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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       34.26        32.02        69.34        69.96        23.24        19.43 
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        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       24.59        75.81        28.90       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
       34.55        43.56         8.28        30.61        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA 
       34.82        32.88        36.82        22.29        34.16        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       39.55        41.62        35.77        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        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 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.72        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       38.07        32.91        30.44        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OW 
       18.21        18.90        13.25        16.57        28.77        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 
       29.95        29.85        40.41        41.13        39.78        23.11 
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-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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30        33.21         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-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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
       13.28        10.62        32.75        17.06        15.32        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       22.26         2.63         7.46        19.53        19.59        17.49 
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-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-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG 
       47.01        64.21         0.16         0.26        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       21.07        13.84        17.39        17.26        17.03         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        29.03        15.35        16.04       107.05 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.03              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           165.76            282.90 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           25.035            28.500 
[1] "0.0 - 165.8 (25.0)" "0.0 - 282.9 (28.5)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED        12        8        0        0        60        33
  6Q GAIN WILD-TYPE      77       75        6        6       292       220
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  6Q GAIN MUTATED           0         19          6          8        2       0
  6Q GAIN WILD-TYPE         2        136         21         57       18      13
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 8                75
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               60               292
  STAGE IIB               33               220
  STAGE III                0                 2
  STAGE IIIA              19               136
  STAGE IIIB               6                21
  STAGE IIIC               8                57
  STAGE IV                 2                18
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    27  95  21   6
  6Q GAIN WILD-TYPE 247 530 116  34
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              27               247
  T2              95               530
  T3              21               116
  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
  6Q GAIN MUTATED    85  37  17   9
  6Q GAIN WILD-TYPE 421 321 102  68
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              85               421
  N1              37               321
  N2              17               102
  N3               9                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED   126   2
  6Q GAIN WILD-TYPE 763  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    126    2
  6Q GAIN WILD-TYPE  763   20
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0             126               763
  1               2                20
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED   148   1
  6Q GAIN WILD-TYPE 919  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    148    1
  6Q GAIN WILD-TYPE  919   11
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE             148               919
  MALE                 1                11
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    57  78
  6Q GAIN WILD-TYPE 380 469
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     57   78
  6Q GAIN WILD-TYPE  380  469
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               57               380
  YES              78               469
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q GAIN MUTATED                            0                           117
  6Q GAIN WILD-TYPE                          1                           651
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q GAIN MUTATED                               15                   5
  6Q GAIN WILD-TYPE                            186                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q GAIN MUTATED                       4                                4
  6Q GAIN WILD-TYPE                     5                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  6Q GAIN MUTATED                    1              3
  6Q GAIN WILD-TYPE                 16             43
D12V9, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                117               651
  INFILTRATING LOBULAR CARCINOMA                15               186
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 3                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"
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                          34    94
  6Q GAIN WILD-TYPE                       147   650
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                     34               147
  WHITE                                         94               650
[1] 4 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     7 116
  6Q GAIN WILD-TYPE  32 758
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  116
  6Q GAIN WILD-TYPE   32  758
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             116               758
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   268  43
  7P GAIN WILD-TYPE 649 105
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              311               754 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               43               105 
$`7P GAIN MUTATED`
TCGA-A2-A1G4 TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A8-A093 TCGA-A8-A09K 
       19.56        23.61        24.26        23.80        17.95        29.98 
TCGA-AC-A3W5 TCGA-AC-A5EI TCGA-AQ-A54O TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM 
       16.57        14.53        32.91        17.23        57.27        73.35 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-D8-A146 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LL-A440 
       54.05        32.58        21.14        52.96        75.02        24.95 
TCGA-LL-A740 TCGA-S3-AA17 TCGA-W8-A86G TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF 
       14.50        13.94        11.41       133.05       131.67        48.10 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CV TCGA-A2-A0CW 
       20.88        13.68        39.32       101.98        98.99       107.93 
TCGA-A2-A0D0 TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 
       67.33        31.82        63.29        44.88        17.13         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25B 
       18.21        21.90        18.61        23.47        20.25        42.44 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 
       33.93        91.07        50.37        26.96        35.31        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A425 
       35.67        33.11        31.73        20.19        25.15        14.70 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV 
       13.74        14.50        21.17        17.92        12.10        10.29 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
        1.02        17.98        31.00        26.01         1.02        53.98 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08P 
       18.97         8.98        24.99        28.96        19.96        31.00 
TCGA-A8-A08X TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M 
       43.00        41.98        12.00         9.99        12.00        33.07 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ 
       14.01        12.00        73.91         5.72        26.04        14.66 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC 
       14.96        11.44        17.42        13.58         1.68         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A049 TCGA-AN-A0AL TCGA-AN-A0FT 
       20.19         1.12         2.30         0.62         7.46         7.04 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J3 TCGA-AO-A0J6 
        0.36         0.33         5.36        66.77        21.40        37.48 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 
       50.70        72.00        55.33       115.27       113.62       106.78 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 
       98.27        82.68        70.42        61.87        82.62        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AV 
       32.52         5.26        65.36        83.87       134.14        61.28 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A5QP 
      160.90        50.89       104.28        50.96        89.00        38.96 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH 
      143.38       281.29        11.90       129.57        50.70       112.37 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV TCGA-B6-A0WV 
      127.33        84.59       255.68       234.28       169.51        79.46 
TCGA-B6-A0WZ TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      206.86        85.35        62.93        20.45        25.55        63.09 
TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT 
       39.16        37.22        21.70        74.89        75.48        77.75 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS 
       74.14        46.39        81.73        78.28        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GY 
       79.00         4.41         9.63        81.83        24.49        30.35 
TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W7 
       23.08        13.61        36.85        50.79         5.59        44.81 
TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX 
       90.84        51.16        69.93        91.99        12.00        49.58 
TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A5J0 
       97.48        33.17        72.07        26.14        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
        9.63         5.26        11.93        11.77        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A131 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A26X TCGA-C8-A26Y 
       48.53        13.51        12.49        11.28        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JF 
       15.45        16.87        33.99        14.17        14.17        12.03 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XL 
       53.00        20.12        20.09        23.90        15.22        19.92 
TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K 
       15.85        12.99        16.54        15.32         9.93        48.03 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P 
       33.37        18.51        34.42        37.51        40.11        40.96 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A153 
       38.60        75.98        34.26        32.02        69.96        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-A15I TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD 
       55.63        11.05        56.94        76.57        32.35        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LI 
       33.73        33.70        60.99        19.66        28.90       102.61 
TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N3 
       43.04         8.28        30.61        34.92        17.69        34.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R3 
       34.16        36.20        41.62        35.24        24.82         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 
        6.12        48.23        45.01        32.09        40.24        34.45 
TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO 
       41.72        38.99         7.13        24.56        12.33        38.07 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P0 
       30.44        23.90         8.48        28.77        22.82        41.13 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 
       29.82        23.11         7.86        18.90        19.99        17.52 
TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DL TCGA-GM-A3XN 
        7.40        79.10        83.34        70.85       115.69        66.38 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP 
        2.60        11.84        10.62        32.75        15.32        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW 
        2.63        16.08        17.49        58.52        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66N 
       28.87        22.32        26.70        23.47        41.92        26.04 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF 
       14.07        28.21         8.91        86.96         0.16        18.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 
       21.07        20.68        17.03         3.81        29.03 

$`7P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 
      107.70        38.30        31.36        21.73        22.32        11.28 
TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 
       11.97        11.05        53.06        29.03        19.99        15.06 
TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
       33.01        33.01        33.01         1.02        49.05        45.07 
TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       19.79        19.33        13.71        50.24        17.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-BH-A18H 
        2.56        19.20        98.33        66.15        81.63        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
       89.16         9.70        10.42        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LD-A74U 
       73.64        50.07        26.99        15.68        85.35        13.22 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA12 TCGA-WT-AB41 
       29.23        25.05        14.79        40.08        18.87        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      108.07        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
       14.37        43.43        14.27        47.24        31.79         7.96 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       73.84        87.25        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48       107.93        77.19        75.25         5.19 
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-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      134.40        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        61.94        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        50.43        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-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-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        56.28        47.31        35.93        50.83 
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-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26G 
       34.29        35.47        30.61        29.79        29.56        23.74 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA 
       20.61        11.34        10.59        10.29        13.41        14.93 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       14.73        10.72         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I 
       13.02        17.03         9.01        43.00        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W 
       12.00        32.05         9.99        10.98         7.99         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-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       12.00        37.05         9.99        31.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q 
       40.01        30.97         9.99        50.04         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        19.23 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       22.95        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X 
       16.80        18.67        12.26         8.22         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         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-A0FX TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO 
        6.90         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-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       69.83        58.95        44.42        32.78        52.18        26.04 
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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 
       65.10        26.24        62.04        71.80       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
      102.31        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ 
       11.51        24.79        26.93       130.09       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      107.24       133.22       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       37.81        94.29        86.53        86.43        33.73        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
      105.27       102.84       105.30        98.76        98.66        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       93.30        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IG 
       33.30        10.59        77.62       275.87        65.52       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      233.62        18.77       165.76       129.07       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      212.25        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT 
      140.28       100.70        89.46       282.90        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.01       113.79       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.55        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
      170.17        37.87         7.07        74.99        68.12        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 
      103.63        71.15        59.84        81.44        39.55        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       84.13        51.68        32.02        18.21        43.53        61.51 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        72.23        74.14        76.60        85.87        49.94 
TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       77.95        41.75        89.06        90.97        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       38.01        29.98        13.91         3.22        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI 
       16.27        15.68        14.30        44.81        31.00        63.32 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        63.39        53.26        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-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA 
       51.32        27.25        23.93        24.95        42.35        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
       32.91         4.90        35.93        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-A1EW TCGA-BH-A1EY 
       51.39       113.82        82.85        42.28        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       25.81        31.53        25.08       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
      122.83        33.99        63.35        55.00        45.63        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       55.50        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 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        12.66        12.56        12.16        12.59 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.92        12.46        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       12.53        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 
       20.88        13.25        20.58        13.97        13.48        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        55.50        15.78        18.15        18.90 
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-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        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-A1XS 
       21.83        14.50        17.69        55.30        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.64        15.16        43.04        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L 
       17.42        16.04        13.45        13.05        14.43        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48        17.06         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       12.26        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        46.59        40.41        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y 
       44.68        38.24        33.17        43.33        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15F 
       18.51        63.62        21.04        23.87        22.82        21.63 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15S 
       12.92        53.92         9.04        20.58        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE 
       51.39        53.62        87.22        33.01        28.50        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        70.36        28.44        59.18         3.88        22.19 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       11.08        54.18        60.36        24.59        75.81       106.75 
TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 
        8.75        34.55        43.56        38.76        34.29        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        22.29        36.56        39.55        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 
       18.94         9.86        28.27        34.95         3.02        11.15 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JS 
       40.73        40.50        20.12         0.69         1.94        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
        9.47        32.91        30.18        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       25.81        26.40        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        16.57        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD 
       40.41        39.78        18.48        30.08         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-EW-A6S9 
       25.91        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN 
      216.76        72.10        85.15        86.96       106.06       101.62 
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-A7W5 TCGA-LD-A7W6 
       18.12        62.47        11.57        21.24         7.10        13.28 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       17.06        14.70        14.47        15.68         7.46        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       12.36        19.59        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66L 
       31.99        58.62        24.72        20.38        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-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        9.93        18.48        19.27        13.84        17.39        17.26 
TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        15.35        16.04       107.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           281.29            282.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           28.210            28.205 
[1] "0.0 - 281.3 (28.2)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        19       22        3        2       113        68
  7P GAIN WILD-TYPE      70       61        3        4       239       185
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  7P GAIN MUTATED           0         41          9         23        7       5
  7P GAIN WILD-TYPE         2        114         18         42       13       8
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                22                61
  STAGE IB                 3                 3
  STAGE II                 2                 4
  STAGE IIA              113               239
  STAGE IIB               68               185
  STAGE III                0                 2
  STAGE IIIA              41               114
  STAGE IIIB               9                18
  STAGE IIIC              23                42
  STAGE IV                 7                13
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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    73 184  40  14
  7P GAIN WILD-TYPE 201 441  97  26
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              73               201
  T2             184               441
  T3              40                97
  T4              14                26
[1] 4 2
[1] TRUE
[1] "dimension 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   147 100  31  26
  7P GAIN WILD-TYPE 359 258  88  51
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             147               359
  N1             100               258
  N2              31                88
  N3              26                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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   246   7
  7P GAIN WILD-TYPE 643  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    246    7
  7P GAIN WILD-TYPE  643   15
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             246               643
  1               7                15
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   306   7
  7P GAIN WILD-TYPE 761   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    306    7
  7P GAIN WILD-TYPE  761    5
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             306               761
  MALE                 7                 5
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   120 168
  7P GAIN WILD-TYPE 317 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    120  168
  7P GAIN WILD-TYPE  317  379
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              120               317
  YES             168               379
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P GAIN MUTATED                            1                           241
  7P GAIN WILD-TYPE                          0                           527
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P GAIN MUTATED                               42                   1
  7P GAIN WILD-TYPE                            159                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P GAIN MUTATED                       5                                8
  7P GAIN WILD-TYPE                     4                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  7P GAIN MUTATED                    2             13
  7P GAIN WILD-TYPE                 15             33
D13V9, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                241               527
  INFILTRATING LOBULAR CARCINOMA                42               159
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                13                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"
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                          60   211
  7P GAIN WILD-TYPE                       121   533
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                     60               121
  WHITE                                        211               533
[1] 4 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     9 251
  7P GAIN WILD-TYPE  30 623
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  251
  7P GAIN WILD-TYPE   30  623
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             251               623
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   233  34
  7Q GAIN WILD-TYPE 684 114
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              267               798 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               34               114 
$`7Q GAIN MUTATED`
TCGA-A2-A1G4 TCGA-A7-A13G TCGA-A7-A26F TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 
       19.56        23.61        24.26        33.01        33.01        17.95 
TCGA-AC-A3W5 TCGA-AC-A5EI TCGA-AC-A62X TCGA-AQ-A54O TCGA-AR-A1AR TCGA-AR-A2LR 
       16.57        14.53        13.71        32.91        17.23        57.27 
TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-D8-A146 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.35        54.05        32.58        21.14        52.96        75.02 
TCGA-LL-A440 TCGA-LL-A740 TCGA-W8-A86G TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF 
       24.95        14.50        11.41       133.05       131.67        48.10 
TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       20.88        39.32       101.98        98.99       107.93        67.33 
TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0YE 
       33.76        31.82        63.29        44.88         8.38        18.21 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A3XS 
       21.90        18.61        23.47        20.25        42.44        33.93 
TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA 
       91.07        50.37        26.96        35.31        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A425 TCGA-A7-A4SB 
       33.11        31.73        20.19        25.15        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-A07R TCGA-A8-A07U TCGA-A8-A07W 
       17.98        26.01        18.97         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       45.07        28.96        19.96        37.05        31.00         0.99 
TCGA-A8-A08X TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q 
       43.00        41.98         9.99        12.00        33.07        25.02 
TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A5XU 
       14.01        73.91         5.72        26.04        14.66        14.96 
TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS 
       17.42         1.68         0.03        20.19         1.12         2.30 
TCGA-AN-A0FL TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J2 
        7.59         0.36         0.33         5.36        66.77        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12B 
       52.18        37.48        72.00       115.27       113.62        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 
       82.68        70.42        60.56        61.87        82.62        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24Q 
       32.52         5.26       108.36        61.28        50.89       104.28 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       93.83        39.39        38.96       143.38       281.29        11.90 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV 
      112.37       233.62       127.33       255.68       234.28       169.51 
TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AU 
       79.46       206.86        85.35        74.99        18.84        62.93 
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        74.89        75.48 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DP 
       77.75        74.14        46.39        81.73        78.28        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB 
        2.56        79.00         4.41         9.63        81.83        24.49 
TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       36.85         5.59        90.84        51.16        69.93        91.99 
TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12P 
       49.58        97.48        18.64         9.63         5.26        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A1HN 
       12.66        12.66        48.53        12.59        11.28        12.95 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A143 
       12.36        12.95        15.45        16.87        33.99        14.17 
TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF 
       14.17        12.03        53.00        20.12        20.09        15.22 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.54        15.32         9.93        48.03        33.37        18.51 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T 
       34.42        37.51        40.11        40.96        38.60        75.98 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A 
       34.26        69.96        23.24        19.43        25.05        23.34 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15R TCGA-E2-A1AZ 
       17.29        20.71        18.21        55.63        56.94        76.57 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 
       37.25        33.73        33.70        19.66         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       34.92        17.69        34.82        34.16        39.55        41.62 
TCGA-E9-A1QZ TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A247 
       24.82        45.01        32.09        34.45        41.72        38.99 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 
        7.13        12.33        30.44        23.90         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 
       22.82        23.11         7.86        18.90        19.99        17.52 
TCGA-EW-A6SB TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A3XL 
       24.99         7.40        79.10        83.34        70.85        69.30 
TCGA-GM-A3XN TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM 
       66.38         2.60        11.84        10.62        32.75        15.32 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5RV 
       22.26         2.63        16.08        17.49        58.52        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K 
       36.36        28.87        22.32        26.70        23.47        41.92 
TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF 
       26.04        28.21         8.91        86.96         0.16        18.81 
TCGA-S3-A6ZH TCGA-UU-A93S TCGA-WT-AB44 
       21.07         3.81        29.03 

$`7Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
      107.70        38.30        31.36        23.80        21.73        22.32 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E 
       11.28        11.97        11.05        53.06        29.03        19.99 
TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       15.06        33.01         1.02        49.05        45.07        29.98 
TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       19.79        19.33        50.24        17.79         5.65         2.56 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-BH-A18H TCGA-BH-A1F5 
       19.20        98.33        66.15        81.63        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
        9.70        10.42        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A442 
       50.07        26.99        15.68        85.35        13.22        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 
       25.05        14.79        40.08        18.87        13.94        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      108.07        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK 
       14.37        43.43        14.27        47.24        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        73.84        87.25        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       24.79       114.81        92.48       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
        5.19        56.81        34.55        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       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        61.94        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       27.12        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-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 
       23.77        17.36        60.72        22.45        19.20        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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13H 
       21.90        34.29        35.47        30.61        29.79        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A4SA TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.93        14.73        10.72         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       13.02        13.02        31.00         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        43.00        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
        9.99        10.98         7.99        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T 
        0.99        38.01        12.00         9.99        31.00       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09N 
       40.01        30.97        12.00         9.99        50.04         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 
       19.23        22.95        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       19.33        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       29.26        16.80        11.44        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-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 
        7.46         0.16         0.33         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         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ 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-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        81.63        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       58.95        44.42        21.40        26.04        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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A128 
       26.24        62.04        55.33        71.80       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
      108.03       102.31        53.88        40.57        20.45        97.08 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ 
       11.51        24.79        26.93       130.09       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        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       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      125.16       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       93.90        99.32        37.81        94.29        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       85.64        71.05       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 
       63.62        38.17        40.54        33.30        10.59        77.62 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
      275.87       129.57        50.70        65.52       146.50        18.77 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       165.76       129.07       140.88        68.45       212.25 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       282.90        97.48       188.68        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.55        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       37.87         7.07        68.12       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       25.55        63.09        81.44        39.55        70.22        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM 
       51.68        32.02        18.21        43.53        61.51        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       72.23        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        89.06        90.97        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       29.98        13.91         3.22        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       15.68        14.30        44.81        31.00        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        63.39        53.26        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-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       13.61        12.89        51.32        27.25        50.79        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        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        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-A1ES 
       55.63        37.55        66.05         7.36        51.39       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        12.00        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        25.08       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 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        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-A42T 
       57.83       130.16        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      110.60        20.88        23.51        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W 
       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-A135 
       12.66        12.56        12.16        13.51        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
       12.46        12.49        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 
       12.03        12.33        12.33        20.25        12.53        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        24.56        14.43        12.95        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        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.58        13.97        13.48        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        18.15        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-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-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        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.31        16.64        12.99        15.16        43.04        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-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        16.41        13.48        17.06         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.53        12.26        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E 
       25.22        43.00        27.52        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U 
       28.87        47.15        44.68        38.24        33.17        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 
       32.02        31.96        69.34        18.51        63.62        21.04 
TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       23.87        22.82        21.63        12.92        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        11.05        19.56        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF 
       87.22        33.01        32.35        28.50        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       70.36        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        60.36        24.59        75.81        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        34.55        43.56 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       38.76        34.29        32.88        36.82        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       36.56        35.77        35.24        25.84        18.94         9.86 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        40.73        40.50        20.12         0.69 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        1.94        24.56        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       27.85        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD 
       39.78        29.82        18.48        30.08         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-EW-A6S9 
       25.91        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        31.30        33.21       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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
      110.50        38.20        43.73        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A5YL 
       62.47        11.57        21.24         7.10        13.28        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.70        14.47        15.68         7.46        19.53        12.36 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       19.59        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O 
       58.62        24.72        20.38        65.62        42.77        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY 
       14.07        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-AA14 
        9.93        18.48        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.26        17.03        66.84        15.35        16.04       107.05 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           281.29            282.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            28.87             27.96 
[1] "0.0 - 281.3 (28.9)" "0.0 - 282.9 (28.0)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        15       21        3        2        99        57
  7Q GAIN WILD-TYPE      74       62        3        4       253       196
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  7Q GAIN MUTATED           0         31          9         20        7       3
  7Q GAIN WILD-TYPE         2        124         18         45       13      10
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                21                62
  STAGE IB                 3                 3
  STAGE II                 2                 4
  STAGE IIA               99               253
  STAGE IIB               57               196
  STAGE III                0                 2
  STAGE IIIA              31               124
  STAGE IIIB               9                18
  STAGE IIIC              20                45
  STAGE IV                 7                13
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    64 157  31  14
  7Q GAIN WILD-TYPE 210 468 106  26
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              64               210
  T2             157               468
  T3              31               106
  T4              14                26
[1] 4 2
[1] TRUE
[1] "dimension 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   130  81  26  23
  7Q GAIN WILD-TYPE 376 277  93  54
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             130               376
  N1              81               277
  N2              26                93
  N3              23                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   210   7
  7Q GAIN WILD-TYPE 679  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    210    7
  7Q GAIN WILD-TYPE  679   15
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             210               679
  1               7                15
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   263   5
  7Q GAIN WILD-TYPE 804   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    263    5
  7Q GAIN WILD-TYPE  804    7
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             263               804
  MALE                 5                 7
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   107 143
  7Q GAIN WILD-TYPE 330 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    107  143
  7Q GAIN WILD-TYPE  330  404
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              107               330
  YES             143               404
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q GAIN MUTATED                            1                           206
  7Q GAIN WILD-TYPE                          0                           562
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q GAIN MUTATED                               37                   2
  7Q GAIN WILD-TYPE                            164                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q GAIN MUTATED                       5                                6
  7Q GAIN WILD-TYPE                     4                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  7Q GAIN MUTATED                    2              9
  7Q GAIN WILD-TYPE                 15             37
D14V9, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                206               562
  INFILTRATING LOBULAR CARCINOMA                37               164
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 9                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"
D14V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0    15
  7Q GAIN WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          59   170
  7Q GAIN WILD-TYPE                       122   574
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                45
  BLACK OR AFRICAN AMERICAN                     59               122
  WHITE                                        170               574
[1] 4 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     7 214
  7Q GAIN WILD-TYPE  32 660
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  214
  7Q GAIN WILD-TYPE   32  660
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             214               660
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   241  46
  8P GAIN WILD-TYPE 676 102
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              287               778 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               46               102 
$`8P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A426 TCGA-A8-A093 
       38.30        24.26        23.80        21.73        11.97        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-AC-A5EI TCGA-AC-A62X TCGA-AO-A0JI TCGA-AQ-A54N 
        1.02        49.05        14.53        13.71        50.24         2.56 
TCGA-AQ-A54O TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A1F5 TCGA-E2-A2P5 TCGA-GM-A2DD 
       32.91        66.15        57.27        89.16        26.99        75.02 
TCGA-GM-A2DO TCGA-LL-A740 TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU 
       85.35        14.50        18.87        11.41        52.96       133.05 
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK 
      131.67         9.96        43.43        14.27        13.68        31.79 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
      143.15       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-A0YE 
       27.12        44.88         8.38        17.46        18.90        18.21 
TCGA-A2-A0YJ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A259 TCGA-A2-A3KD TCGA-A2-A3XS 
       18.61        20.25        19.20        52.47        39.65        33.93 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CJ 
       47.31        35.93        24.39        26.96        21.14        30.61 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3J0 TCGA-A7-A4SA 
       35.67        29.79        25.15        23.74        10.29        14.93 
TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       14.50        10.72        10.29        10.42         8.75        13.02 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        43.00        18.97 
TCGA-A8-A07O TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08R 
        9.99         9.99        18.05        13.02        28.96         0.99 
TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09X 
      112.08        30.97         9.99        12.00        33.07        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BM 
       19.04        27.02        17.03        22.95        73.91        99.35 
TCGA-AC-A2FE TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3YI TCGA-AC-A62V 
       86.66        26.04        14.66         6.48        23.24        11.44 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A0AJ 
       13.58         1.68         0.03         0.33         0.33         9.96 
TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XS TCGA-AO-A03R 
        7.00         7.04         0.36         0.33         0.33        68.75 
TCGA-AO-A03T TCGA-AO-A0J7 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       69.83        20.32       108.03        98.27        70.42        60.56 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AR-A0U0 TCGA-AR-A0U4 
       97.08        61.87        11.51        32.52        65.36       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R 
      125.16       108.36        99.32        33.73       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       97.84        50.96        99.62        85.64        71.05        93.83 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.25        54.21        33.30        38.96       281.29       275.87 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL 
      129.57        65.52       112.37       255.68       212.25        81.17 
TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KC 
       78.02       102.77       169.51        21.01       245.10        43.59 
TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
      101.52       170.17         7.07        85.35        74.99        62.93 
TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0C1 
       20.45        39.55        39.16        37.22        18.21        46.39 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       15.65         2.56        79.00        15.68        14.30        44.81 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HQ 
       30.35        10.78        15.16        24.56        26.50        36.85 
TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A1EO 
       12.89         5.59        44.81        23.05        26.66        91.99 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FC 
      113.82        42.28        12.00        49.58       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A5J0 
       74.73       122.83        45.63        26.14        83.31        23.51 
TCGA-BH-A6R8 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
        9.63        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A26X TCGA-C8-A273 TCGA-D8-A141 
       12.16        12.92         0.16        12.36        16.87        20.58 
TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU 
       13.97        15.78        12.03        14.01        21.01        14.70 
TCGA-D8-A1X6 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU 
       17.79        18.15        15.22        14.50        19.92        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I 
       43.04        16.54        15.32         9.93        14.14        14.43 
TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14U TCGA-E2-A14Y 
       12.53        34.42        46.59        44.68        43.33        69.34 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15S 
       69.96        19.43        25.05        17.29        21.63        14.07 
TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IN TCGA-E2-A573 TCGA-E2-A576 
       76.57        28.50        37.25        22.19        34.92        34.29 
TCGA-E9-A1N5 TCGA-E9-A1NE TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
       36.82        35.77         2.56        11.15        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A228 TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       40.24        42.25        20.12        38.99        12.33        29.72 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J1 
       30.44        23.90        26.70        26.40         8.48        18.90 
TCGA-EW-A1J6 TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC 
       28.77        41.13        23.11        18.48        19.99         6.15 
TCGA-EW-A6SA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-HN-A2NL TCGA-LL-A5YO TCGA-LL-A73Y 
       16.77        83.34        70.85         2.60        14.47        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I 
        7.46        19.53        58.52        31.99        58.62        23.47 
TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-S3-AA10 
       26.04        28.21        40.11        18.48        19.27 

$`8P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A3J1 
       19.56       107.70        23.61        31.36        22.32        11.28 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F 
       11.05        53.06        29.03        19.99        15.06        33.01 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
       33.01        33.01        45.07        29.98        16.57        19.79 
TCGA-AC-A5XS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       19.33        17.79         5.65        19.20        98.33        17.23 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A8FY 
       73.35        81.63        54.05        32.58        21.44         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       50.07        15.68        52.96        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA17 TCGA-Z7-A8R5 TCGA-3C-AALJ 
       25.05        14.79        40.08        13.94       108.07        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SH 
       47.61        11.44         8.52        14.37        48.10        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04P 
       20.88         7.96        39.32        28.01        18.21        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       78.41        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
       99.12       114.81        92.48       107.93        77.19         5.19 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
      107.93        34.55        25.22       101.72       134.40       118.45 
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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       63.29        99.19        54.64        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.13        49.84        20.52        20.75        32.55        25.28 
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-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-A3KC TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       36.23        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE 
       50.83         7.30        21.30        23.21        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       34.29        35.47        37.45        33.11        31.73        20.19 
TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 
       29.56        20.61        11.34        10.59        13.41        14.70 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VW 
       13.74        21.17        17.92        14.73        12.10         9.37 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07G 
       13.02         1.02        17.98        31.00        17.03        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       14.01        12.00        32.05        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08G 
       24.99        45.07        36.95         0.99        38.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08X 
       12.00        37.05         9.99        31.00        31.00        43.00 
TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09N 
       40.01        41.98        12.00         9.99        50.04         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H 
       13.02        21.04         0.99        38.04        19.23         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       22.26        73.05        40.57        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       74.14        33.04        19.33        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YJ 
       22.19        24.13        25.05        14.99        15.48        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       29.26        16.80        14.96        17.42        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A041 
        8.22        20.19         1.12         1.32         2.30         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.46         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-A0FV 
        5.65         7.96         7.59         7.17         6.90         0.33 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR 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-A03U TCGA-AO-A03V 
       61.35        66.77        81.63        95.70        58.95        44.42 
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-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       65.10        26.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12G 
      113.62       108.72       106.78       102.31        82.68        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       40.57        20.45        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       15.62       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86       107.24       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
       83.87       134.14       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        93.90        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43       160.90        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
      118.59         2.76       105.27       102.84       105.30        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM 
       98.66        89.00        93.30       166.42        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       38.17        39.39        40.54        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       11.90        50.70       146.50       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI 
       84.59       165.76       129.07       140.88        68.45       234.28 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       162.05       140.28       100.70        89.46       282.90 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        79.46        18.35       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN 
      129.70        28.27        68.94        58.55        73.51       139.17 
TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       37.87        68.12        18.84       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       25.55        63.09        81.44        70.22        84.13        51.68 
TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        77.95        74.14        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
       78.28         3.22        67.86        70.88        16.27         4.41 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H3 
        9.63        81.83        24.49        31.00        63.32        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK 
       53.26        23.08        41.00        52.96        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
        2.50        13.61        51.32        27.25        50.79        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        32.91         4.90        35.93        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-A1EN TCGA-BH-A1ET 
       66.05         7.36        51.39        51.16        69.93        82.85 
TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       55.69        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
       33.17        33.99        63.35        55.00        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       55.50        28.14        38.60        57.83       130.16        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       36.79        20.12        10.52       110.60        20.88        18.64 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        5.26        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       11.77        11.77        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.59        12.46        12.49        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.34        11.28        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 
       20.25        12.53        12.95        15.45        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        20.88        13.25 
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-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ 
       55.50        18.15        18.90        53.00        18.97        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-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       18.58        16.73        25.74        23.90        27.58        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       17.16        14.73        21.83        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       15.85        16.31        16.64        15.16        15.52        14.24 
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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.48        17.06         1.61        10.09        13.08        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        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       43.00        27.52        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-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 
       75.98        34.26        32.02        31.96        18.51        63.62 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E 
       23.24        21.04        23.87        23.34        22.82        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       11.05        19.56        56.94        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       33.01        32.35        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        38.76        17.69        34.82        32.88 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       22.29        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE 
       34.95         6.12         3.02        48.23         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
       40.50         0.69         1.94         7.13        24.56         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO 
       38.07        32.91        30.18        23.84         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        12.20        39.72        18.21        13.25        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 
       25.94        22.82        29.95        29.85        40.41        39.78 
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-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       24.99        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        79.10        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        15.32        14.70        22.26         2.63        16.08 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       36.30        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-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       14.07        19.73         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-AA0Z 
        0.16         0.26         9.93        18.81        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           281.29            282.90 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            26.40             29.03 
[1] "0.0 - 281.3 (26.4)" "0.0 - 282.9 (29.0)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        22       25        2        2        95        69
  8P GAIN WILD-TYPE      67       58        4        4       257       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  8P GAIN MUTATED           2         37          8         14        8       5
  8P GAIN WILD-TYPE         0        118         19         51       12       8
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 22                67
  STAGE IA                25                58
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               95               257
  STAGE IIB               69               184
  STAGE III                2                 0
  STAGE IIIA              37               118
  STAGE IIIB               8                19
  STAGE IIIC              14                51
  STAGE IV                 8                12
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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    76 164  39   9
  8P GAIN WILD-TYPE 198 461  98  31
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              76               198
  T2             164               461
  T3              39                98
  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   138  99  28  18
  8P GAIN WILD-TYPE 368 259  91  59
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             138               368
  N1              99               259
  N2              28                91
  N3              18                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   239   9
  8P GAIN WILD-TYPE 650  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    239    9
  8P GAIN WILD-TYPE  650   13
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             239               650
  1               9                13
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   286   5
  8P GAIN WILD-TYPE 781   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    286    5
  8P GAIN WILD-TYPE  781    7
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE             286               781
  MALE                 5                 7
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   110 152
  8P GAIN WILD-TYPE 327 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    110  152
  8P GAIN WILD-TYPE  327  395
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              110               327
  YES             152               395
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P GAIN MUTATED                            0                           218
  8P GAIN WILD-TYPE                          1                           550
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P GAIN MUTATED                               39                   3
  8P GAIN WILD-TYPE                            162                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P GAIN MUTATED                       5                                9
  8P GAIN WILD-TYPE                     4                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  8P GAIN MUTATED                    4             12
  8P GAIN WILD-TYPE                 13             34
D15V9, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                218               550
  INFILTRATING LOBULAR CARCINOMA                39               162
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             4                13
  OTHER, SPECIFY                                12                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"
D15V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    14
  8P GAIN WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          61   188
  8P GAIN WILD-TYPE                       120   556
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                46
  BLACK OR AFRICAN AMERICAN                     61               120
  WHITE                                        188               556
[1] 4 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     9 228
  8P GAIN WILD-TYPE  30 646
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  228
  8P GAIN WILD-TYPE   30  646
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             228               646
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   444  77
  8Q GAIN WILD-TYPE 473  71
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              521               544 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               77                71 
$`8Q GAIN MUTATED`
TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A7-A26F TCGA-A7-A26H 
       19.20        36.13        19.56        38.30        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A426 TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S 
       21.73        22.32        11.97        53.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-AC-A5EI 
       33.01        17.95         1.02        49.05        29.98        14.53 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL 
       13.71        50.24        17.79         2.56        32.91        66.15 
TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-BH-A1F5 TCGA-E2-A15O TCGA-E2-A2P5 TCGA-EW-A1P3 
       57.27        81.63        89.16        50.79        26.99        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LL-A5YP TCGA-LL-A740 TCGA-S3-AA12 TCGA-W8-A86G 
       75.02        85.35        14.79        14.50        18.87        11.41 
TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE 
       52.96       133.05       131.67         9.96        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A2-A04N 
       48.10        14.27        13.68        31.79        39.32       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP 
       78.41       121.94        73.84        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-A259 TCGA-A2-A25B 
       17.36        60.72        20.25        19.20        52.47        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX 
       18.15       105.34        39.65        33.93        29.98        47.31 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       35.93        50.83        24.39        26.96        21.14        21.90 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G 
       30.61        35.67        29.79        31.73        25.15        23.74 
TCGA-A7-A3J0 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       10.29        14.93        14.50        21.17        12.10        10.72 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       10.29        10.42         8.75        13.02        13.02        17.98 
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-A07F TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       18.97        14.01         9.99        10.98         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
        9.99        18.05        13.02        28.96        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A092 
       37.05        31.00         0.99       112.08        43.00        30.97 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
        9.99        12.00        33.07         1.02        25.02         8.98 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
        0.99        14.01        19.04         0.99        27.02        17.03 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FE 
       22.95        73.91         5.72        73.05        99.35        86.66 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3YI TCGA-AC-A62V 
       26.04        33.04        14.66         6.48        23.24        11.44 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
       13.58         1.68         0.03        20.19         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        0.62         1.78         1.71         9.96         0.16         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         7.59         7.04         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AO-A03O 
        0.33         5.36         0.33        12.33         0.33        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       68.75        69.83        44.42        21.40        52.18        26.04 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       20.32       106.78       108.03        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       60.56        53.88        97.08        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       24.79       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AI 
       84.10       109.02        98.93        65.36       107.21       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AW 
      101.00       103.86        93.90        99.32        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       86.43        33.73       160.90       104.28       112.77        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 
      102.84       105.30        50.96        98.66        99.62        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN 
       71.05        93.83        20.25        54.21        39.39        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       38.96        10.59        77.62       143.38       281.29       275.87 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE 
      129.57        65.52       112.37       127.33        84.59       255.68 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV 
      212.25        81.17        78.02       102.77       282.90       169.51 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC 
       18.35        21.01       113.79       245.10        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
      101.52       170.17         7.07        85.35        74.99        18.84 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B4 
       62.93        59.84        20.45        25.55        39.55        39.16 
TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT 
       37.22        18.21        61.51        74.89        75.48        77.75 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS 
       41.75        46.39        81.73        78.28        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GZ 
       79.00        16.27        15.68        14.30        44.81        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU 
       15.16        24.56        23.08        26.50        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25        50.79         5.59        42.35        44.81        23.05 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       35.93        26.66        37.74        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 
      113.82        42.28        12.00        55.69        49.58        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM 
       97.48       120.62       114.15        74.73       122.83        45.63 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A5J0 
       55.50        26.14        83.31       130.16        20.88        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
        9.63        18.87        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 
       12.66        12.66        12.66        12.16        13.51        12.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.34         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A8HR 
       12.36        15.45        16.87         0.03        24.56        13.41 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JC TCGA-D8-A1JD 
       20.58        13.97        14.17        19.20        15.78        18.15 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        53.00        14.01        20.09        20.12        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XB 
       21.01        13.32        14.70        18.58        17.79        18.15 
TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU 
       15.22        14.50        19.92        16.41        16.31        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R 
       14.14        13.05        14.43        16.41        13.48        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14N 
       12.53        12.26        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        75.98        43.33        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 
       69.34        18.51        69.96        23.24        19.43        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15J 
       23.34        22.82        17.29        20.71        21.63        53.92 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       11.05        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO 
       32.35        28.50        37.25        33.70        22.19        60.99 
TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z 
       60.36        24.59       106.75       102.61         8.75         8.28 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        38.76        34.29        17.69        36.82        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       36.20        35.77        35.24         9.86        34.95         2.56 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG 
       11.15        45.01        32.09        40.24        46.65        21.27 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       39.09        38.37        41.72        20.12        38.99         1.94 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       12.33        29.72        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW 
       26.70        26.40         8.48        18.90        28.77        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 
       29.85        40.41        41.13        23.11        18.48         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A6SA TCGA-EW-A6SB 
       19.99         6.15        13.94        19.96        16.77        24.99 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A3XL TCGA-GM-A5PV 
       33.21       109.87        83.34        70.85        69.30        13.55 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A5YN 
        2.60        11.84        11.57         7.10        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        16.08        15.68         7.46        19.53        12.36 
TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I TCGA-OL-A66N 
       17.49        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        18.81        18.48        19.27 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-Z7-A8R6 
       17.03         3.81        66.84        15.35       107.05 

$`8Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A25A TCGA-A7-A13G 
       48.56        48.36        63.12        88.60       107.70        23.61 
TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 
       31.36        11.28        11.05        29.03        19.99        15.06 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 
       45.07        16.57        19.79        19.33         5.65        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       98.33        17.23        73.35        54.05        32.58        21.44 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 
        9.70        10.42        21.14        14.79        16.47        73.64 
TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       50.07        15.68        13.22        24.95        29.23        25.05 
TCGA-OL-A5RU TCGA-S3-AA17 TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
       40.08        13.94       108.07        48.46        47.61        11.44 
TCGA-A1-A0SB TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ 
        8.52        47.24        20.88         7.96        28.01        18.21 
TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CO 
       18.02        87.25       101.98        55.43       136.73       114.81 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        77.19         5.19       107.93       101.72       134.40 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW 
      118.45        74.40        72.00        35.05        31.82        61.94 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0YC TCGA-A2-A0YD 
       99.19        54.64        44.28        20.52        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G6 
       50.47        49.48        19.33        48.46        22.45        16.47 
TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       17.19        10.59        36.23        91.07        32.75        56.28 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG 
       50.37         7.30        21.30        23.21        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26J 
       35.47        37.45        33.11        20.19        29.56        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SF 
       11.34        10.59        13.41        14.70        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A07G TCGA-A8-A07J 
       14.73         9.37         1.02        31.00        18.97        12.00 
TCGA-A8-A07L TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B 
       32.05         7.99        45.07        36.95         0.99        38.01 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
        9.99        31.00        40.01        41.98        12.00         9.99 
TCGA-A8-A09D TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 
       50.04        19.04        15.02        12.00        13.02        21.04 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       38.04        19.23        22.26        40.57        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       87.12        74.14        19.33        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YJ 
       22.19        24.13        25.05        14.99        15.48        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       29.26        16.80        14.96        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         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XP 
        5.65         7.96         7.17         6.90         0.33         0.30 
TCGA-AN-A0XR 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-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 
       61.35        66.77        95.70        58.95        32.78        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        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12H TCGA-AO-A1KO 
      115.27       113.62       108.72       102.31        40.57        20.45 
TCGA-AQ-A04J TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       26.93         5.26        75.22        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AN 
      133.22        83.87       134.14       125.16        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.07        37.81        61.28        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A250 
       99.78       118.59         2.76       105.27        98.76        89.00 
TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       93.30       166.42        86.53        63.62        38.17        40.54 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO 
       11.90        50.70       146.50       233.62        18.77       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO 
      129.07       140.88        68.45       234.28       263.28       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      140.28       100.70        89.46        97.48       188.68        79.46 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KI TCGA-B6-A1KN 
      206.86       129.70        28.27        68.94        73.51       139.17 
TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B0 
       37.87        68.12       103.63        71.15        63.09        81.44 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
       70.22        84.13        51.68        32.02        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        72.23        74.14        76.60        85.87        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       77.95        74.14        89.06        90.97        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       38.01        29.98        13.91         3.22        67.86        70.88 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        4.41         9.63        81.83        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI 
       30.35        63.39        53.26        41.00        52.96        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 
        5.85         2.50        13.61        51.32        23.93        24.95 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P 
       32.91         4.90        20.12        90.84        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ET 
       55.63        37.55        66.05         7.36        69.93        82.85 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ 
       17.69        25.81        25.08        33.17        33.99        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 
       55.00        72.07        53.98        28.14        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ 
       36.82        36.79        20.12        10.52       110.60        18.64 
TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q 
        5.26        21.76         9.44        11.93        11.77        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
       48.53        12.56        12.59        12.59        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       12.33        10.92        11.28        20.25        12.53        12.95 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
       16.70         9.76        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A145 
       12.49        19.46        56.81        20.88        13.25        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JI 
       14.17        17.49        16.50        55.50        18.90        18.97 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       19.40        20.38        12.20        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM 
       27.58        12.39        17.16        14.73        21.83        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27F 
       55.30        15.85        16.64        15.16        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 
       13.45        48.03        17.06         1.61        13.08        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        12.66        25.22        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        63.62        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        55.63         9.04        20.58        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       87.22        33.01        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       28.44        59.18         3.88        11.08        54.18        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       75.81        28.90        43.04        34.55        43.56        30.61 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        34.16        36.56        39.55        41.62 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 
       25.84        18.94        24.82        28.27         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       48.23         1.12         6.58        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       32.05        42.25        37.74        41.03        40.73        40.50 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        0.69         7.13        24.56         9.47        38.07        32.91 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
        0.79        25.81        27.85        12.20        39.72        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P4 
       13.25        16.57        25.94        29.95        39.78        29.82 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
       30.08        18.90        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-A423 
       52.73        25.91        22.09        34.03        17.49        17.52 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        15.22        31.30         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       79.10        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       18.12        62.47        21.24        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
       17.06        22.26         2.63        19.59        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
        2.10        36.30        34.92        36.36        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        20.38        26.70        65.62        41.92        42.77 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE 
       17.36        14.07        19.73         8.91        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        21.07        20.68        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-WT-AB44 TCGA-XX-A89A 
       17.39        17.26        29.03        16.04 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.16 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           282.90            263.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           26.040            29.965 
[1] "0.0 - 282.9 (26.0)" "0.2 - 263.3 (30.0)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        44       37        3        3       181       110
  8Q GAIN WILD-TYPE      45       46        3        3       171       143
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  8Q GAIN MUTATED           2         79         15         32       11       8
  8Q GAIN WILD-TYPE         0         76         12         33        9       5
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 44                45
  STAGE IA                37                46
  STAGE IB                 3                 3
  STAGE II                 3                 3
  STAGE IIA              181               171
  STAGE IIB              110               143
  STAGE III                2                 0
  STAGE IIIA              79                76
  STAGE IIIB              15                12
  STAGE IIIC              32                33
  STAGE IV                11                 9
  STAGE X                  8                 5
[1] 12  2
[1] TRUE
[1] "dimension of 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   136 312  57  21
  8Q GAIN WILD-TYPE 138 313  80  19
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1             136               138
  T2             312               313
  T3              57                80
  T4              21                19
[1] 4 2
[1] TRUE
[1] "dimension 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   248 162  67  39
  8Q GAIN WILD-TYPE 258 196  52  38
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             248               258
  N1             162               196
  N2              67                52
  N3              39                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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   448  12
  8Q GAIN WILD-TYPE 441  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    448   12
  8Q GAIN WILD-TYPE  441   10
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             448               441
  1              12                10
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   521   8
  8Q GAIN WILD-TYPE 546   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    521    8
  8Q GAIN WILD-TYPE  546    4
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             521               546
  MALE                 8                 4
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   197 279
  8Q GAIN WILD-TYPE 240 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    197  279
  8Q GAIN WILD-TYPE  240  268
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              197               240
  YES             279               268
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q GAIN MUTATED                            1                           416
  8Q GAIN WILD-TYPE                          0                           352
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q GAIN MUTATED                               59                   5
  8Q GAIN WILD-TYPE                            142                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q GAIN MUTATED                       6                               14
  8Q GAIN WILD-TYPE                     3                               16
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  8Q GAIN MUTATED                    5             22
  8Q GAIN WILD-TYPE                 12             24
D16V9, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                416               352
  INFILTRATING LOBULAR CARCINOMA                59               142
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          6                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)              14                16
  MUCINOUS CARCINOMA                             5                12
  OTHER, SPECIFY                                22                24
[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"
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1    29
  8Q GAIN WILD-TYPE                                0    31
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                         106   338
  8Q GAIN WILD-TYPE                        75   406
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         29                31
  BLACK OR AFRICAN AMERICAN                    106                75
  WHITE                                        338               406
[1] 4 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    13 425
  8Q GAIN WILD-TYPE  26 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13  425
  8Q GAIN WILD-TYPE   26  449
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                26
  NOT HISPANIC OR LATINO             425               449
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED   114  23
  9P GAIN WILD-TYPE 803 125
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              137               928 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               23               125 
$`9P GAIN MUTATED`
TCGA-A8-A093 TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AQ-A54N TCGA-BH-A0EA TCGA-D8-A146 
       17.95        16.57        13.71         2.56        32.58        21.14 
TCGA-E2-A158 TCGA-E2-A2P5 TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U 
       14.79        26.99        11.44        31.79        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SX TCGA-A2-A0T2 
      101.98        24.79        77.19        98.99        50.43         8.38 
TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25D TCGA-A2-A4S2 TCGA-A7-A0DB 
       49.84        31.73        23.47        18.15        21.14        33.11 
TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VX 
       20.19        10.29        14.70        14.50        14.73        10.42 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C 
       18.97         8.98        24.99        45.07        38.01        28.96 
TCGA-A8-A08X TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2FM 
       43.00        14.01        22.95         5.72        73.05        26.04 
TCGA-AC-A8OQ TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
        1.12         0.33         7.00         7.04         0.33         0.33 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JL TCGA-AO-A128 TCGA-AR-A0U0 TCGA-AR-A1AY 
       20.32        53.03        55.33       106.78        65.36        33.73 
TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ 
      160.90        89.00        93.83       143.38       112.37       233.62 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A0X1 
      140.88       255.68       100.70       282.90       206.86       245.10 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BG 
       43.59        73.51        25.55        51.68        37.22        61.51 
TCGA-BH-A0BT TCGA-BH-A0EE TCGA-BH-A0RX TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18V 
       77.75        31.00         5.59        32.91        55.63        51.16 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A202 
       42.28        12.00        25.81        97.48       114.15        26.14 
TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A26Z TCGA-D8-A141 
       18.64         5.26        12.59        12.49        15.45        20.58 
TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF 
       14.17        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        43.04        12.53        18.51 
TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1BD 
       37.51        47.15        19.43        25.05        76.57        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A9RU 
       33.73        33.70        19.66        43.04         8.28        17.69 
TCGA-E9-A1N6 TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1P8 
       22.29         0.69        38.07         8.48        18.90         7.86 
TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL 
        6.15        34.55        19.96        70.85        72.10        69.30 
TCGA-GM-A4E0 TCGA-LL-A5YM TCGA-LL-A6FR TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I 
       72.03        15.32        16.08        22.39        36.36        23.47 
TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       28.21        86.96         9.93        18.81        20.68 

$`9P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S 
       53.06        29.03        19.99        15.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W6 
       33.01         1.02        49.05        45.07        29.98        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O 
       14.53        19.33        50.24        17.79         5.65        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       19.20        98.33        17.23        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       81.63        54.05        21.44        89.16         9.70        10.42 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 
       50.79        16.47        73.64        50.07        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       14.79        14.50        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       52.96       108.07       133.05       131.67        48.46        47.61 
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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04X 
       18.21       143.15        18.02        78.41       121.94        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CT 
      136.73        99.12       114.81        92.48       107.93        75.25 
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-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72       134.40        80.28       118.45 
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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.88        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F 
       16.47        52.47        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 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         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-A0DA TCGA-A7-A0DC 
       34.29        35.47        30.61        37.45        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       31.73        25.15        29.56        23.74        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       10.59        13.41        14.93        13.74        21.17        17.92 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O 
       12.10        10.72        10.29         9.37         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98         9.01        43.00        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W 
       12.00        32.05         9.99        10.98         7.99         9.99 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08I 
       18.05        36.95        13.02         0.99        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       40.01        30.97        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       12.00        50.04        33.07         1.02        25.02         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        19.23 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       73.91        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       16.80        14.96        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-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-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AS 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-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.59         7.17         6.90         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         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        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        32.78        21.40        52.18        26.04        37.48 
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-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       65.10        26.24        62.04        71.80       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       108.03       102.31        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       60.56        53.88        40.57        20.45        97.08        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       82.62        11.51        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86       107.24       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       37.81        94.29        61.28        86.53        86.43        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        99.62        93.30        85.64        71.05 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       102.77       140.28        89.46       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.46        18.35        21.01       113.79       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.55       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
       37.87         7.07        85.35        74.99        68.12        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ 
      103.63        71.15        62.93        59.84        20.45        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BC 
       81.44        39.55        39.16        70.22        84.13        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       81.83        24.49        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        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         4.90        35.93        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-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-A1F2 TCGA-BH-A1F8 
       82.85        55.69        49.58        17.69        31.53        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.83        33.99        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        53.98        55.50        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       110.60        20.88        23.51         9.63 
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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        48.53        12.56        12.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.92        12.46        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36        12.95        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        20.88        13.25 
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-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        12.03        53.00        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        55.30        16.41        15.85        16.31        16.64 
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 
       48.03        16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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        75.98        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        69.34        18.51        63.62        69.96        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        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE 
       53.62        87.22        33.01        32.35        28.50        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        70.36        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB 
       60.99        11.08        54.18        60.36        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90       106.75       102.61         8.75        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        38.76        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        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        12.33        29.72         9.47        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 
       26.40        27.85        12.20        39.72        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        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-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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.52        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       33.21         7.40       109.87        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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX 
      110.50        38.20        43.73        66.38        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 
        2.60        62.47        11.84        11.57        21.24         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       13.28        10.62        32.75        17.06        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26         2.63        15.68         7.46        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       19.59        17.49        27.91         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       31.99        58.62        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-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-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 
       64.21         0.16         0.26        18.48        21.07        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.33              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           282.90            281.29 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            25.05             28.82 
[1] "0.3 - 282.9 (25.1)" "0.0 - 281.3 (28.8)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         9        6        1        2        55        35
  9P GAIN WILD-TYPE      80       77        5        4       297       218
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  9P GAIN MUTATED           0         10          4         12        2       1
  9P GAIN WILD-TYPE         2        145         23         53       18      12
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 6                77
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               55               297
  STAGE IIB               35               218
  STAGE III                0                 2
  STAGE IIIA              10               145
  STAGE IIIB               4                23
  STAGE IIIC              12                53
  STAGE IV                 2                18
  STAGE X                  1                12
[1] 12  2
[1] TRUE
[1] "dimension of 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  89  14   7
  9P GAIN WILD-TYPE 246 536 123  33
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              28               246
  T2              89               536
  T3              14               123
  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
  9P GAIN MUTATED    66  48   9  14
  9P GAIN WILD-TYPE 440 310 110  63
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              66               440
  N1              48               310
  N2               9               110
  N3              14                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED   115   3
  9P GAIN WILD-TYPE 774  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    115    3
  9P GAIN WILD-TYPE  774   19
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0             115               774
  1               3                19
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED   139   0
  9P GAIN WILD-TYPE 928  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    139    0
  9P GAIN WILD-TYPE  928   12
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE             139               928
  MALE                 0                12
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    53  75
  9P GAIN WILD-TYPE 384 472
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     53   75
  9P GAIN WILD-TYPE  384  472
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               53               384
  YES              75               472
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P GAIN MUTATED                            0                           109
  9P GAIN WILD-TYPE                          1                           659
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P GAIN MUTATED                               20                   2
  9P GAIN WILD-TYPE                            181                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P GAIN MUTATED                       1                                1
  9P GAIN WILD-TYPE                     8                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  9P GAIN MUTATED                    1              5
  9P GAIN WILD-TYPE                 16             41
D17V9, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                109               659
  INFILTRATING LOBULAR CARCINOMA                20               181
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 5                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"
D17V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     7
  9P GAIN WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          30    93
  9P GAIN WILD-TYPE                       151   651
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     30               151
  WHITE                                         93               651
[1] 4 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     5 113
  9P GAIN WILD-TYPE  34 761
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5  113
  9P GAIN WILD-TYPE   34  761
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             113               761
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED   100  21
  9Q GAIN WILD-TYPE 817 127
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              121               944 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               127 
$`9Q GAIN MUTATED`
TCGA-A8-A093 TCGA-AC-A62X TCGA-AR-A5QM TCGA-BH-A0EA TCGA-BH-A18H TCGA-D8-A146 
       17.95        13.71        73.35        32.58        21.44        21.14 
TCGA-E2-A2P5 TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U 
       26.99        48.46        11.44        31.79        73.84        87.25 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV 
       77.19        98.99         8.38        49.84        31.73        23.47 
TCGA-A2-A25B TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 
       42.44        21.14        33.11        20.19        10.29        14.70 
TCGA-A7-A6VX TCGA-A8-A07F TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A09X 
       10.42        18.97        45.07        38.01        28.96        14.01 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A5XU TCGA-AN-A04A TCGA-AN-A0FK 
       22.95         5.72        26.04        14.96         2.96         7.00 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A128 
        7.04         0.33         0.33         0.33        20.32       106.78 
TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A1AJ TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 
       24.79         5.26       101.00       160.90        89.00        93.83 
TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RS 
      143.38       112.37       233.62        18.77       140.88       100.70 
TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0BA TCGA-BH-A0BG 
      282.90       206.86        73.51        25.55        37.22        61.51 
TCGA-BH-A0DQ TCGA-BH-A0E9 TCGA-BH-A18F TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV 
        3.22        81.83        32.91        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 
       12.59        12.49        11.34        12.03        12.95         0.03 
TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       13.02        20.58        14.17        18.15        18.90        53.00 
TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A27V 
       13.32        18.15        15.22        19.92        12.99        12.53 
TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A1BD TCGA-E2-A1II 
       18.51        37.51        47.15        19.43        37.25        33.70 
TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A22E 
       19.66        43.04         8.28        17.69        22.29        41.72 
TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1P4 TCGA-EW-A1P8 
        0.69        38.07         8.48        18.90        29.82         7.86 
TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A3XL 
        6.15        34.55        19.96         7.40        70.85        69.30 
TCGA-LL-A6FR TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I TCGA-PE-A5DE TCGA-S3-AA0Z 
       16.08        22.39        36.36        23.47        86.96        20.68 
TCGA-Z7-A8R6 
      107.05 

$`9Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S 
       53.06        29.03        19.99        15.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01         1.02        49.05        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       19.79        14.53        19.33        50.24        17.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
        2.56        32.91        19.20        98.33        17.23        66.15 
TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       57.27        81.63        54.05        89.16         9.70        10.42 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 
       14.79        50.79        16.47        73.64        50.07        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK 
       11.41        52.96       108.07       133.05       131.67        47.61 
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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04W 
       18.21       143.15        18.02        78.41       121.94       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        75.25         5.19       107.93        56.81        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       118.45        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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       17.13        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-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        19.33        48.46        23.77        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C 
       22.45        20.25        19.20        16.47        52.47        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        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         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-A13F TCGA-A7-A13H 
       37.45        35.67        29.79        31.73        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A4SA 
       23.74        20.61        11.34        10.59        13.41        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-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.72        10.29         9.37         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        17.98        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G 
        9.99        18.05        36.95        13.02         0.99        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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 
      112.08        43.00        40.01        30.97        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
        9.99         9.99        12.00        50.04        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04        19.23        73.91        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       40.57        86.66        90.71        60.92        87.12        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       33.04        19.33        14.66        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y 
       23.24        24.79        29.26        16.80        11.44        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-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-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         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         7.46         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         6.90 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XS 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-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 
       69.83        58.95        44.42        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        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        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       115.27       113.62       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      102.31        98.27        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        20.45        97.08        61.87        82.62        11.51 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        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       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      125.16       108.36       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
      102.84       105.30        50.96        98.76        98.66        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59        77.62       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN 
      129.57        50.70        65.52       146.50       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      165.76       129.07       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55        43.59       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        74.99        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        59.84        20.45        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        70.22        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        74.14        41.75        46.39        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       78.28        15.65         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         4.90        35.93 
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-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99       113.82        82.85        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        97.48        25.08       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.83        33.99        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-A208 
       53.98        55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       20.88        23.51         9.63        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       13.51        12.59        12.92        12.46        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.28         0.16        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 
       12.53        12.36        15.45        16.87        16.70         9.76 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
       24.56        14.43        33.99        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 
       19.46        56.81        20.88        13.25        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        55.50        15.78 
TCGA-D8-A1JF 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-A1X5 
       19.40        20.38        21.01        12.20        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-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31        16.64        15.16        43.04 
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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       12.26        33.37        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
       43.00        34.42        27.52        46.59        40.41        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        75.98        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-A155 
       69.34        18.51        63.62        69.96        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        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        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       77.65        37.41        70.36        33.73        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90       106.75       102.61         8.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56        30.61        34.92        38.76        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        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        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       41.03        40.73        40.50        20.12        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        7.13        24.56        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       25.81        26.40        27.85        12.20        39.72        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        40.41        41.13        39.78        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-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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.52        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21       109.87        59.57       216.76        79.10        83.34 
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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        17.06        15.32 
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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       19.53        12.36        19.59        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX 
       36.30        58.52        31.99        58.62        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-PL-A8LX TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        21.07        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       17.39        17.26        17.03         3.81        66.84        29.03 
TCGA-XX-A899 TCGA-XX-A89A 
       15.35        16.04 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           282.90            281.29 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           22.290            28.965 
[1] "0.0 - 282.9 (22.3)" "0.0 - 281.3 (29.0)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         8        4        1        2        48        32
  9Q GAIN WILD-TYPE      81       79        5        4       304       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  9Q GAIN MUTATED           0         12          5          7        2       0
  9Q GAIN WILD-TYPE         2        143         22         58       18      13
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  8                81
  STAGE IA                 4                79
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               48               304
  STAGE IIB               32               221
  STAGE III                0                 2
  STAGE IIIA              12               143
  STAGE IIIB               5                22
  STAGE IIIC               7                58
  STAGE IV                 2                18
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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  80  13   6
  9Q GAIN WILD-TYPE 251 545 124  34
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              23               251
  T2              80               545
  T3              13               124
  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    58  45   9   9
  9Q GAIN WILD-TYPE 448 313 110  68
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              58               448
  N1              45               313
  N2               9               110
  N3               9                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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED   102   2
  9Q GAIN WILD-TYPE 787  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    102    2
  9Q GAIN WILD-TYPE  787   20
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0             102               787
  1               2                20
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED   122   0
  9Q GAIN WILD-TYPE 945  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    122    0
  9Q GAIN WILD-TYPE  945   12
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE             122               945
  MALE                 0                12
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    47  67
  9Q GAIN WILD-TYPE 390 480
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     47   67
  9Q GAIN WILD-TYPE  390  480
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               47               390
  YES              67               480
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q GAIN MUTATED                            0                            93
  9Q GAIN WILD-TYPE                          1                           675
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q GAIN MUTATED                               18                   3
  9Q GAIN WILD-TYPE                            183                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q GAIN MUTATED                       2                                1
  9Q GAIN WILD-TYPE                     7                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  9Q GAIN MUTATED                    1              4
  9Q GAIN WILD-TYPE                 16             42
D18V9, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 93               675
  INFILTRATING LOBULAR CARCINOMA                18               183
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 4                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"
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                          21    84
  9Q GAIN WILD-TYPE                       160   660
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                     21               160
  WHITE                                         84               660
[1] 4 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     4 103
  9Q GAIN WILD-TYPE  35 771
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4  103
  9Q GAIN WILD-TYPE   35  771
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                35
  NOT HISPANIC OR LATINO             103               771
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED   174  32
  10P GAIN WILD-TYPE 743 116
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               206                859 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                32                116 
$`10P GAIN MUTATED`
TCGA-A7-A26I TCGA-A8-A09E TCGA-AC-A62X TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       21.73        49.05        13.71         2.56        32.91        19.20 
TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-BH-A0EA TCGA-E2-A2P5 TCGA-S3-AA17 TCGA-A1-A0SE 
       66.15        81.63        32.58        26.99        13.94        43.43 
TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D2 
       48.10        28.01        78.41        87.25        24.79        33.76 
TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 
       79.76        31.82        44.88        50.43        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25B 
       49.84        21.90        18.61        31.73        19.20        42.44 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G 
       33.93        91.07        35.67        31.73        20.19        23.74 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O 
       14.93        14.50        17.92        14.73        10.29        13.02 
TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A07U 
        1.02        31.00        17.03        43.00         8.98        24.99 
TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X 
       45.07        38.01        19.96        37.05        31.00        43.00 
TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E 
       30.97         9.99        50.04        25.02        14.01        22.95 
TCGA-AC-A2BK TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS 
       73.05        11.44         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        44.42        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       115.27       106.78       102.31        82.62        11.51 
TCGA-AQ-A04L TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ 
      130.09        84.10       109.02       107.21       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
      103.86        99.32        86.53        33.73       160.90        50.89 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE 
       97.84       102.84       105.30        99.62       129.57        65.52 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      112.37       233.62        84.59       165.76       140.88       255.68 
TCGA-B6-A0RO TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 TCGA-B6-A409 
      162.05       245.10        43.59       101.52        74.99        18.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0DS 
       20.45        25.55        61.51        74.89        41.75         2.56 
TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HU 
       79.00         9.63        44.81        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-A26X TCGA-C8-A274 TCGA-C8-A27B 
       12.66        12.16        13.51        12.36        16.70        14.43 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD 
       13.02        20.88        13.97        19.20        55.50        18.15 
TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1XW 
       12.03        20.09        18.58        15.22        12.99        43.04 
TCGA-D8-A1XZ TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14R 
       15.32        18.51        34.42        47.15        44.68        38.60 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A1AZ 
       63.62        69.96        19.43        25.05        18.21        76.57 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
      106.75       102.61         8.75        34.92        38.76        22.29 
TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A247 
       36.20        32.09        46.59        41.03         0.69        38.99 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       12.33        30.18        26.40        28.77        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       40.41        19.99         6.15        19.96        52.73        25.91 
TCGA-EW-A423 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH 
       17.52        24.99       109.87        79.10        70.85        72.10 
TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A73Z 
       11.84         7.10        10.62        15.32         2.63         7.46 
TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-S3-AA0Z TCGA-S3-AA10 
       19.59        22.39        20.38        28.21        20.68        19.27 
TCGA-UL-AAZ6 TCGA-UU-A93S 
       17.03         3.81 

$`10P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
       17.95         1.02        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AR-A1AM 
       14.53        19.33        50.24        17.79         5.65        98.33 
TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A18H TCGA-BH-A1F5 
       17.23        57.27        73.35        54.05        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       73.64        50.07        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU 
       40.08        18.87        11.41        52.96       108.07       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK 
       14.37        14.27        47.24        20.88        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R 
        7.96        39.32        18.21       143.15        18.02       121.94 
TCGA-A2-A04T TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       73.84       101.98        55.43       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48       107.93        77.19        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       118.45        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-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-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-A1G6 TCGA-A2-A259 
       17.36        60.72        22.45        20.25        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        36.23        39.65 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         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-A0CJ 
       21.14        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J 
       37.45        33.11        29.79        25.15        29.56        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB 
       11.34        10.59        10.29        13.41        14.70        13.74 
TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       21.17        12.10        10.72         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       13.02        17.98        26.01         1.02        53.98         9.01 
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-A07W TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
       10.98         7.99         9.99        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
        0.99        28.96        12.00         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
      112.08        40.01        41.98        12.00         9.99        12.00 
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        19.23        73.91         5.72        22.26 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       14.96        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ 
        0.33         0.23         0.33         0.62         2.96         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         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         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J5 
       95.70        68.75        69.83        58.95        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-A0JJ TCGA-AO-A0JM 
       72.00        76.77        65.10        26.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      113.62       108.72       108.03        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       60.56        53.88        40.57        20.45        97.08        61.87 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       24.79        26.93        15.62        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AL 
       65.36       133.22        83.87       134.14       125.16        97.68 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       96.00        86.07        93.90        37.81        94.29        61.28 
TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       86.43        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      104.28       112.77       105.27        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
      281.29        11.90       275.87        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      127.33       129.07        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       263.28       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       58.55        73.51       139.17       170.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        68.12       103.63        71.15        62.93        59.84 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       63.09        81.44        39.55        39.16        70.22        84.13 
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        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       77.75        49.94        77.95        74.14        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       13.91        78.28        15.65         3.22        67.86        70.88 
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        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        63.32        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
        2.50        13.61        36.85        51.32        27.25        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        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        49.58        17.69        25.81 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.08       120.62        33.17        74.73       122.83        33.99 
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        53.98        55.50 
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 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       18.64        23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        48.53        12.56        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
       20.25        12.53        12.95        15.45        16.87         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.76        24.56        33.99        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       19.46        56.81        13.25        20.58        14.17        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG 
       14.17        17.49        16.50        15.78        18.90        53.00 
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-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-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       16.41        15.85        16.31        16.64        15.16        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        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       17.06         1.61        10.09        13.08        12.53        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        12.66        25.22        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-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       28.87        40.96        38.24        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 
       34.26        32.02        31.96        69.34        18.51        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       11.05        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 
       19.66        24.59        75.81        28.90        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       43.56         8.28        30.61        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        36.82        34.16        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        45.01        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        38.37        41.72        40.73        40.50        20.12 
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         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       18.90        13.25        16.57        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-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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       22.09        34.03        17.49        23.51        15.22        16.77 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       31.30        33.21         7.40        59.57       216.76        83.34 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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-A3YX TCGA-LD-A66U TCGA-LD-A7W6 
       18.12         2.60        62.47        11.57        21.24        13.28 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
       32.75        17.06        14.70        14.47        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       15.68        19.53        12.36        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        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-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-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-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 
        0.26         9.93        18.81        18.48        21.07        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.39        17.26        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.33               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            255.68             282.90 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            30.985             27.520 
[1] "0.3 - 255.7 (31.0)" "0.0 - 282.9 (27.5)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED        17       11        1        1        76        40
  10P GAIN WILD-TYPE      72       72        5        5       276       213
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           0         30          7         12        7
  10P GAIN WILD-TYPE         2        125         20         53       13
                    vv
clus                 STAGE X
  10P GAIN MUTATED         3
  10P GAIN WILD-TYPE      10
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                 11                 72
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                76                276
  STAGE IIB                40                213
  STAGE III                 0                  2
  STAGE IIIA               30                125
  STAGE IIIB                7                 20
  STAGE IIIC               12                 53
  STAGE IV                  7                 13
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    45 127  23  12
  10P GAIN WILD-TYPE 229 498 114  28
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               45                229
  T2              127                498
  T3               23                114
  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   103  57  27  16
  10P GAIN WILD-TYPE 403 301  92  61
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0              103                403
  N1               57                301
  N2               27                 92
  N3               16                 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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   176   8
  10P GAIN WILD-TYPE 713  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    176    8
  10P GAIN WILD-TYPE  713   14
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0              176                713
  1                8                 14
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   206   2
  10P GAIN WILD-TYPE 861  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    206    2
  10P GAIN WILD-TYPE  861   10
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE              206                861
  MALE                  2                 10
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    82 109
  10P GAIN WILD-TYPE 355 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     82  109
  10P GAIN WILD-TYPE  355  438
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                82                355
  YES              109                438
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P GAIN MUTATED                            0                           177
  10P GAIN WILD-TYPE                          1                           591
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P GAIN MUTATED                               16                   4
  10P GAIN WILD-TYPE                            185                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P GAIN MUTATED                       1                                4
  10P GAIN WILD-TYPE                     8                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  10P GAIN MUTATED                    0              6
  10P GAIN WILD-TYPE                 17             40
D19V9, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 177                591
  INFILTRATING LOBULAR CARCINOMA                 16                185
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  6                 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"
D19V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1    10
  10P GAIN WILD-TYPE                                0    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          51   126
  10P GAIN WILD-TYPE                       130   618
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          10                 50
  BLACK OR AFRICAN AMERICAN                      51                130
  WHITE                                         126                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"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7 164
  10P GAIN WILD-TYPE  32 710
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7  164
  10P GAIN WILD-TYPE   32  710
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              164                710
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    93  19
  10Q GAIN WILD-TYPE 824 129
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               112                953 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                19                129 
$`10Q GAIN MUTATED`
TCGA-A7-A26I TCGA-AC-A62X TCGA-AQ-A54N TCGA-BH-A0B6 TCGA-BH-A0EA TCGA-E2-A2P5 
       21.73        13.71         2.56        81.63        32.58        26.99 
TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0EQ 
       48.10        28.01        78.41        87.25        24.79        79.76 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A3XS TCGA-A7-A13E TCGA-A7-A26G TCGA-A8-A06O 
       50.43        17.13        33.93        20.19        23.74        13.02 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A092 
       31.00        17.03        45.07        38.01        31.00        30.97 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A62V 
        9.99        50.04        25.02        14.01        22.95        11.44 
TCGA-AN-A04C TCGA-AN-A0FZ TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 
        1.78         0.33        81.63        32.78        21.40        53.03 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AR-A0TS TCGA-AR-A0TT 
      106.78       102.31        11.51       130.09        84.10       109.02 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S 
      108.36       101.00        86.53       160.90        50.89        97.84 
TCGA-AR-A24V TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ 
      105.30       129.57       112.37       233.62       165.76       140.88 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A409 TCGA-BH-A0AY TCGA-BH-A0BL 
      162.05        79.46        43.59        18.84        25.55        74.89 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A18L TCGA-BH-A1EN 
        2.56        79.00         9.63        44.81        26.66        69.93 
TCGA-BH-A1EV TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A274 
       12.00        12.66        11.77        12.66        12.16        16.70 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       13.02        20.88        19.20        55.50        18.15        12.03 
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        63.62        69.96 
TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1LI TCGA-E2-A573 
       19.43        18.21        14.07        76.57       102.61        34.92 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A247 
       22.29        36.20        32.09        46.59        41.03        38.99 
TCGA-E9-A295 TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1PC TCGA-EW-A423 
       12.33        26.40        28.77        25.94         6.15        17.52 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A73Z 
       79.10        72.10        10.62        15.32         2.63         7.46 
TCGA-MS-A51U TCGA-OL-A5S0 TCGA-S3-AA0Z TCGA-S3-AA10 
       22.39        20.38        20.68        19.27 

$`10Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       17.95         1.02        49.05        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       19.79        14.53        19.33        50.24        17.79         5.65 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
       32.91        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       73.35        54.05        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG 
       21.14        14.79        50.79        16.47        73.64        50.07 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       29.23        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI 
       13.94        11.41        52.96       108.07       133.05       131.67 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
       48.46        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK 
       43.43        14.27        47.24        20.88        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R 
        7.96        39.32        18.21       143.15        18.02       121.94 
TCGA-A2-A04T TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       73.84       101.98        55.43       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48       107.93        77.19        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-A0ER 
       25.22       101.72       134.40        80.28       118.45        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-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52         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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.20        16.47        52.47        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        36.23        39.65        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H 
       35.67        33.11        29.79        31.73        25.15        29.56 
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-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-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
       13.02         1.02        17.98        26.01         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        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-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
        9.99        18.05        36.95        13.02         0.99        28.96 
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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
      112.08        43.00        40.01        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00        33.07         1.02         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-A23H 
       27.02        17.03        38.04        19.23        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       29.26        16.80        14.96        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         7.46 
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         6.90         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         5.36         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        69.83        58.95        44.42        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B 
       71.80       115.27       113.62       108.72       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       82.68        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 
       97.08        61.87        82.62        24.79        26.93        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
       32.52       140.55        98.33         5.26        75.22        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       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      134.14       107.21       125.16       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       86.43        33.73        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
        2.76       104.28       112.77       105.27       102.84        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       98.76        98.66        89.00        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.52       146.50        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      129.07       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       263.28       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      282.90       169.51        97.48       188.68        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        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-A0B3 
       62.93        59.84        20.45        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        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        43.53        61.51        21.70        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        74.14        41.75        46.39        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       78.28        15.65         3.22        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
        4.41        15.68        14.30        81.83        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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        32.91         4.90        35.93        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        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        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       110.60        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        5.26        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
       12.36        12.95        15.45        16.87         0.03         9.76 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
       24.56        14.43        33.99        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        56.81        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE 
       13.48        14.17        17.49        16.50        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        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-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.64        12.99        15.16        43.04        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        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        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        12.66        25.22        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 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A 
       18.51        23.24        21.04        23.87        25.05        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        28.90 
TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      106.75         8.75        43.04        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       36.82        34.16        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        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        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       45.01        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.72        40.73        40.50        20.12         0.69 
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         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OW TCGA-EW-A1OX 
       18.21        18.90        13.25        16.57        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        40.41        41.13        39.78        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-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57       216.76        83.34        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
       32.75        17.06        14.70        14.47        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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-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-A6ZG 
       86.96         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       21.07        13.84        17.39        17.26        17.03         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        29.03        15.35        16.04       107.05 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.33               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            233.62             282.90 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             29.87              28.14 
[1] "0.3 - 233.6 (29.9)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         9        7        0        0        38        27
  10Q GAIN WILD-TYPE      80       76        6        6       314       226
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           0         18          5          4        3
  10Q GAIN WILD-TYPE         2        137         22         61       17
                    vv
clus                 STAGE X
  10Q GAIN MUTATED         1
  10Q GAIN WILD-TYPE      12
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  7                 76
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                38                314
  STAGE IIB                27                226
  STAGE III                 0                  2
  STAGE IIIA               18                137
  STAGE IIIB                5                 22
  STAGE IIIC                4                 61
  STAGE IV                  3                 17
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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    23  74  12   5
  10Q GAIN WILD-TYPE 251 551 125  35
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               23                251
  T2               74                551
  T3               12                125
  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    56  34  15   5
  10Q GAIN WILD-TYPE 450 324 104  72
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               56                450
  N1               34                324
  N2               15                104
  N3                5                 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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   100   3
  10Q GAIN WILD-TYPE 789  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    100    3
  10Q GAIN WILD-TYPE  789   19
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0              100                789
  1                3                 19
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   113   1
  10Q GAIN WILD-TYPE 954  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    113    1
  10Q GAIN WILD-TYPE  954   11
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE              113                954
  MALE                  1                 11
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    47  60
  10Q GAIN WILD-TYPE 390 487
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     47   60
  10Q GAIN WILD-TYPE  390  487
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                47                390
  YES               60                487
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q GAIN MUTATED                            0                            96
  10Q GAIN WILD-TYPE                          1                           672
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q GAIN MUTATED                               10                   2
  10Q GAIN WILD-TYPE                            191                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q GAIN MUTATED                       1                                2
  10Q GAIN WILD-TYPE                     8                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  10Q GAIN MUTATED                    0              3
  10Q GAIN WILD-TYPE                 17             43
D20V9, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  96                672
  INFILTRATING LOBULAR CARCINOMA                 10                191
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  3                 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"
D20V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     7
  10Q GAIN WILD-TYPE                                0    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                          22    73
  10Q GAIN WILD-TYPE                       159   671
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      22                159
  WHITE                                          73                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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  88
  10Q GAIN WILD-TYPE  34 786
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   88
  10Q GAIN WILD-TYPE   34  786
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               88                786
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED   123  18
  11P GAIN WILD-TYPE 794 130
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               141                924 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                130 
$`11P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26F TCGA-A8-A091 TCGA-A8-A09K TCGA-AR-A2LR TCGA-BH-A0DO 
       38.30        24.26        33.01        29.98        57.27        54.05 
TCGA-E2-A1BC TCGA-S3-AA17 TCGA-3C-AAAU TCGA-5T-A9QA TCGA-A1-A0SI TCGA-A1-A0SK 
       16.47        13.94       133.05         9.96        20.88        31.79 
TCGA-A1-A0SM TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CT 
        7.96        87.25       101.98        55.43        24.79        75.25 
TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YE 
       67.33        80.28        34.29         8.38        49.84        18.21 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A7-A0CJ TCGA-A7-A0DC 
       17.36        19.20        39.65        91.07        30.61        29.79 
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-A09A TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 
        9.99        33.07        25.02        12.00        21.04         0.99 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A3QQ TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C 
       19.23         5.72        24.13        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         5.36         0.33 
TCGA-AO-A03L TCGA-AO-A0J3 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A1KS 
       80.28        21.40       108.72       102.31        98.27        11.51 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TW TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A250 
      130.09        15.62        98.93        50.89       105.30        89.00 
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        62.93        61.51        21.70        77.75        67.10 
TCGA-BH-A0DP TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18V TCGA-BH-A1EO 
       15.65        63.32        30.35        72.56        51.16        91.99 
TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A27A TCGA-D8-A140 
       26.14        57.83       130.16        12.66        24.56        13.25 
TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 
       12.03        15.22        14.50        16.54        15.52        14.14 
TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15M TCGA-E2-A15R 
       44.68        34.26        69.96        23.34        11.05        56.94 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IU TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R4 
       76.57        33.70        11.08        38.76        34.16         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       11.15        32.09        46.65        20.12         0.69        38.99 
TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P5 
        7.13         0.79        18.90        28.77        29.85        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A6SB TCGA-EW-A6SD 
        7.86        19.99        17.49        17.52        24.99        33.21 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A73Y TCGA-OL-A66I 
       79.10        72.10         2.60        32.75        15.68        23.47 
TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-UU-A93S 
       28.21         9.93         3.81 

$`11P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I 
       19.56       107.70        23.61        31.36        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       49.05        45.07        16.57        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       13.71        50.24        17.79         5.65         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 
       19.20        98.33        17.23        66.15        73.35        81.63 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 
       32.58        21.44        89.16         9.70        10.42        21.14 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 
       14.79        50.79        73.64        50.07        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G 
       25.05        14.79        14.50        40.08        18.87        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
       52.96       108.07       131.67        48.46        47.61        11.44 
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-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       13.68        39.32        28.01        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       78.41       121.94        73.84       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       92.48       107.93        77.19         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       118.45        79.76        74.40        72.00        35.05 
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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        50.43        44.28        17.52        17.13 
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-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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       20.25        16.47        52.47        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        36.23        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         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-A13H TCGA-A7-A3IY TCGA-A7-A3RF 
       31.73        20.19        25.15        29.56        11.34        13.41 
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-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.72        10.29         9.37         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
        1.02        17.98        31.00        26.01         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       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-A09B TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00        50.04         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AB 
        0.99        14.01        19.04        13.02        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04        22.95        73.91        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       16.31        14.83        22.19        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A6IV 
       23.24        24.79        29.26        16.80        14.96        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         7.46 
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-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX 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-A0XT 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        69.83        58.95        44.42 
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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       65.10        26.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      113.62       106.78       108.03        82.68        70.42        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       53.88        40.57        20.45        97.08        61.87        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       24.79        26.93        32.52       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       84.10       109.02        75.22        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       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      102.84        50.96        98.76        98.66        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59        77.62       281.29        11.90       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.52       146.50       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.28        89.46       282.90       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.46        18.35        21.01       113.79       206.86 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.55        43.59       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      139.17       170.17        37.87         7.07        85.35        74.99 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       18.84       103.63        71.15        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       63.09        81.44        39.55        39.16        70.22        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL 
       51.68        37.22        32.02        18.21        43.53        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        81.73        77.98        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       78.28         3.22         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       81.83        24.49        31.00        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        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        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       37.55        66.05         7.36        51.39        69.93       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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        97.48        25.08       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       122.83        33.99        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        53.98        55.50        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.88        18.64        23.51         9.63         5.26        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-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.56        12.16        13.51        12.59        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.46        12.49        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 
       12.49        13.41        19.46        56.81        20.88        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       16.50        55.50        15.78        18.15        18.90        53.00 
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-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
       12.39        17.16        14.73        21.83        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       55.30        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       15.16        43.04        15.32         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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48        17.06         1.61        10.09        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W 
       38.24        38.60        33.17        75.98        43.33        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       31.96        69.34        18.51        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        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        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       20.58        19.56        14.07        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       70.36        33.73        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       60.99        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        34.92        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        22.29        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        24.82        28.27        34.95         2.56         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        45.01        40.24         1.12         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.21        13.25        16.57        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        29.82        18.48        30.08 
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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 
       23.51        15.22        16.77        31.30         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57       216.76        83.34        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24         7.10        13.28        10.62 
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-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       16.08         7.46        19.53        12.36        19.59        17.49 
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-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        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        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       21.07        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.03        66.84        29.03        15.35        16.04       107.05 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.33               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            143.38             282.90 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            24.560             28.685 
[1] "0.3 - 143.4 (24.6)" "0.0 - 282.9 (28.7)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED        11       14        1        2        54        28
  11P GAIN WILD-TYPE      78       69        5        4       298       225
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         15          3          7        4
  11P GAIN WILD-TYPE         2        140         24         58       16
                    vv
clus                 STAGE X
  11P GAIN MUTATED         2
  11P GAIN WILD-TYPE      11
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                 14                 69
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                54                298
  STAGE IIB                28                225
  STAGE III                 0                  2
  STAGE IIIA               15                140
  STAGE IIIB                3                 24
  STAGE IIIC                7                 58
  STAGE IV                  4                 16
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    34  87  15   4
  11P GAIN WILD-TYPE 240 538 122  36
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               34                240
  T2               87                538
  T3               15                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
  11P GAIN MUTATED    76  41  10  10
  11P GAIN WILD-TYPE 430 317 109  67
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               76                430
  N1               41                317
  N2               10                109
  N3               10                 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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED   117   4
  11P GAIN WILD-TYPE 772  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    117    4
  11P GAIN WILD-TYPE  772   18
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0              117                772
  1                4                 18
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED   139   2
  11P GAIN WILD-TYPE 928  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    139    2
  11P GAIN WILD-TYPE  928   10
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE              139                928
  MALE                  2                 10
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    52  76
  11P GAIN WILD-TYPE 385 471
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     52   76
  11P GAIN WILD-TYPE  385  471
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                52                385
  YES               76                471
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P GAIN MUTATED                            0                           113
  11P GAIN WILD-TYPE                          1                           655
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P GAIN MUTATED                               14                   1
  11P GAIN WILD-TYPE                            187                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P GAIN MUTATED                       2                                2
  11P GAIN WILD-TYPE                     7                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  11P GAIN MUTATED                    2              7
  11P GAIN WILD-TYPE                 15             39
D21V9, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 113                655
  INFILTRATING LOBULAR CARCINOMA                 14                187
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  7                 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"
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                          23    98
  11P GAIN WILD-TYPE                       158   646
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                      23                158
  WHITE                                          98                646
[1] 4 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     7 113
  11P GAIN WILD-TYPE  32 761
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7  113
  11P GAIN WILD-TYPE   32  761
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              113                761
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    79  17
  11Q GAIN WILD-TYPE 838 131
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                969 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                131 
$`11Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26F TCGA-BH-A0DO TCGA-5T-A9QA TCGA-A1-A0SI TCGA-A1-A0SK 
       38.30        24.26        54.05         9.96        20.88        31.79 
TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0EY TCGA-A2-A0YE TCGA-A2-A0YJ 
       67.33        80.28        34.29        63.29        18.21        18.61 
TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A6VX 
       19.20        91.07        23.74        10.59        10.29        10.42 
TCGA-A8-A075 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I 
       17.03        18.97        18.97         8.98        38.01        12.00 
TCGA-A8-A09A TCGA-A8-A09Q TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-AC-A62V TCGA-AC-A62Y 
        9.99        25.02        12.00         0.99        11.44        17.42 
TCGA-AN-A04C TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0XU TCGA-AO-A12A TCGA-AO-A12B 
        1.78         7.00         0.33         0.33       102.31        98.27 
TCGA-AQ-A04L TCGA-AR-A0TW TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IE TCGA-B6-A0IO 
      130.09        98.93        50.89       105.30        65.52       165.76 
TCGA-B6-A0RS TCGA-B6-A0X0 TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BJ 
      100.70       129.70        73.51        68.12        61.51        21.70 
TCGA-BH-A0BT TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0GY TCGA-BH-A18M 
       77.75        67.10        29.98        15.65        30.35        72.56 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1FC TCGA-BH-A202 
        7.36        51.39        51.16        91.99       114.15        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XJ 
       38.60        57.83       130.16        13.25        12.03        21.83 
TCGA-D8-A1XK TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-E2-A152 TCGA-E2-A15A 
       14.50        43.04        16.54        14.14        69.96        23.34 
TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A574 TCGA-E9-A1N8 
       56.94        76.57        53.62        33.70        38.76        34.16 
TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J6 
       11.15        32.09         0.69         7.13         0.79        28.77 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-EW-A6SD 
       23.11         7.86        22.09        17.49        24.99        33.21 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LL-A441 TCGA-OL-A66I TCGA-PL-A8LZ TCGA-UU-A93S 
       79.10        72.10        32.75        23.47         9.93         3.81 

$`11Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I 
       19.56       107.70        23.61        31.36        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       19.99        15.06        33.01        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
        1.02        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       14.53        19.33        13.71        50.24        17.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
        2.56        32.91        19.20        98.33        17.23        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       57.27        73.35        81.63        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68         7.96        39.32        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       18.02        78.41       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       22.45        20.25        16.47        52.47        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        36.23        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         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-A0CJ 
       21.14        21.90        35.31        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-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3RF TCGA-A7-A425 
       25.15        29.56        20.61        11.34        13.41        14.70 
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-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O 
       12.10        10.72        10.29         9.37         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       53.98         9.01        43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       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-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       12.00        50.04        33.07         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        14.01        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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79        29.26        16.80        14.96        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         7.46 
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         6.90         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         5.36         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 
       69.83        58.95        44.42        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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      106.78       108.03        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        20.45        97.08        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       24.79        26.93        15.62        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        84.10       109.02        75.22        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       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      105.27       102.84        50.96        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG 
      281.29        11.90       275.87       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       233.62        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.28        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       206.86       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55        43.59       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        85.35        74.99        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        84.13        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        43.53        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS 
       77.98        38.01        13.91        78.28         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        81.83        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       63.32        10.78        15.16        63.39        53.26        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        32.91         4.90        35.93        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-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.83        33.99        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        53.98        55.50        28.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.88        18.64        23.51         9.63         5.26        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-A12Q 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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       20.25        12.53        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       16.70         0.03         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       20.88        20.58        13.97        14.17        13.48        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        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        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-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        12.99        15.16        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-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       48.03        16.41        13.48        17.06         1.61        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        12.66        25.22        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 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        63.62        23.24        19.43        21.04        23.87 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       25.05        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        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       19.56        14.07        51.39        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
        8.28        30.61        34.92        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        22.29        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       41.62        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        45.01        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
       40.50        20.12        38.99         1.94        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70        25.81        26.40        27.85 
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-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       41.13        39.78        29.82        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-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 
       19.96        55.00        52.73        25.91        34.03        17.52 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 
       23.51        15.22        16.77        31.30         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57       216.76        83.34        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       10.62        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63        16.08        15.68         7.46        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        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-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-AA10 
        0.26        18.81        18.48        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 
       13.84        17.39        17.26        17.03        66.84        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.33               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            165.76             282.90 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            27.455             28.210 
[1] "0.3 - 165.8 (27.5)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED        10        5        0        2        36        23
  11Q GAIN WILD-TYPE      79       78        6        4       316       230
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0         10          3          4        2
  11Q GAIN WILD-TYPE         2        145         24         61       18
                    vv
clus                 STAGE X
  11Q GAIN MUTATED         1
  11Q GAIN WILD-TYPE      12
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                  5                 78
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                36                316
  STAGE IIB                23                230
  STAGE III                 0                  2
  STAGE IIIA               10                145
  STAGE IIIB                3                 24
  STAGE IIIC                4                 61
  STAGE IV                  2                 18
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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  62   8   4
  11Q GAIN WILD-TYPE 252 563 129  36
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               22                252
  T2               62                563
  T3                8                129
  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    48  34   7   5
  11Q GAIN WILD-TYPE 458 324 112  72
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               48                458
  N1               34                324
  N2                7                112
  N3                5                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    84   2
  11Q GAIN WILD-TYPE 805  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     84    2
  11Q GAIN WILD-TYPE  805   20
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               84                805
  1                2                 20
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    95   1
  11Q GAIN WILD-TYPE 972  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     95    1
  11Q GAIN WILD-TYPE  972   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               95                972
  MALE                  1                 11
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    29  52
  11Q GAIN WILD-TYPE 408 495
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     29   52
  11Q GAIN WILD-TYPE  408  495
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                29                408
  YES               52                495
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q GAIN MUTATED                            0                            77
  11Q GAIN WILD-TYPE                          1                           691
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q GAIN MUTATED                                5                   2
  11Q GAIN WILD-TYPE                            196                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q GAIN MUTATED                       1                                3
  11Q GAIN WILD-TYPE                     8                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  11Q GAIN MUTATED                    1              7
  11Q GAIN WILD-TYPE                 16             39
D22V9, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  77                691
  INFILTRATING LOBULAR CARCINOMA                  5                196
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  7                 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"
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                          19    66
  11Q GAIN WILD-TYPE                       162   678
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                      19                162
  WHITE                                          66                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"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5  77
  11Q GAIN WILD-TYPE  34 797
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5   77
  11Q GAIN WILD-TYPE   34  797
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               77                797
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   190  32
  12P GAIN WILD-TYPE 727 116
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               222                843 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                116 
$`12P GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A8-A08S TCGA-A8-A09C TCGA-AC-A3W5 TCGA-AC-A62X 
       19.20        38.30        33.01         1.02        16.57        13.71 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A2LR TCGA-AR-A5QM TCGA-E2-A15O TCGA-E2-A2P5 
        5.65        32.91        57.27        73.35        50.79        26.99 
TCGA-GM-A2DD TCGA-LL-A440 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN 
       75.02        24.95       108.07       133.05        48.10        39.32 
TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CU 
       28.01        18.02        73.84        87.25        77.19         5.19 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY 
       56.81        67.33        35.05        34.29        31.82        63.29 
TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25E TCGA-A2-A3XS 
       18.21        21.67        17.36        19.20       105.34        33.93 
TCGA-A2-A3XW TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26J 
       56.28        35.31        29.79        20.19        25.15        20.61 
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-A6VX TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       10.42        53.98         9.01         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A 
       45.07        19.96        37.05        31.00        30.97         9.99 
TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM 
        1.02        14.01        12.00        27.02        22.95        26.04 
TCGA-AC-A2QH TCGA-AC-A5XU TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0FJ TCGA-AN-A0FT 
       33.04        14.96         0.33         1.78         7.96         7.04 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N 
        0.36         0.33         0.33         0.33        80.28        66.77 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A124 TCGA-AO-A12E 
       95.70        32.78        20.32        53.03       115.27        70.42 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A0U4 
       60.56        61.87        11.51        98.33        83.87       107.21 
TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V 
      103.86        99.32        61.28       160.90       104.28       105.30 
TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LM TCGA-B6-A0I2 TCGA-B6-A0IO 
       50.96        98.66        89.00        63.62       143.38       165.76 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI 
      162.05        79.46       113.79       245.10        43.59        73.51 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B5 
        7.07        74.99        68.12        62.93        59.84        70.22 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0DD 
       51.68        37.22        61.51        74.89        77.75        81.73 
TCGA-BH-A0E0 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0HX TCGA-BH-A0WA 
        4.41        44.81        24.49        30.35        27.25        23.05 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO 
       90.84        26.66        37.74        37.55        51.16        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A202 
       42.28        12.00        55.69       114.15        45.63        26.14 
TCGA-BH-A203 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L 
       38.60        18.64        23.51         9.63        18.87        11.93 
TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM 
       12.66        12.66        12.16        11.28        12.03        12.33 
TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 
       15.45         9.76        20.88        14.17        19.20        14.17 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XD TCGA-D8-A1XJ 
       15.78        18.15        20.09        19.40        17.16        21.83 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27M TCGA-D8-A27R 
       12.99        16.54        15.32        15.52        13.48        10.09 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O 
       12.26        18.51        34.42        37.51        40.11        44.68 
TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15S TCGA-E2-A1AZ 
       32.02        69.96        23.34        18.21        14.07        76.57 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 
       33.73        33.70        43.04         8.28        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC 
       36.20        35.24         9.86        11.15        32.09        40.24 
TCGA-E9-A1RG TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       21.27        41.03        20.12        38.99        12.33        29.72 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FV 
       28.77        22.82        29.82        23.11         7.86        25.91 
TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U 
       24.99       109.87        85.15        69.30         2.60        21.24 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV 
        7.10        32.75        22.26         2.63        19.53        34.92 
TCGA-OL-A5RZ TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-UL-AAZ6 
       22.32        17.36        18.81        18.48        19.27        17.03 

$`12P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E 
       19.99        15.06        33.01        33.01        17.95        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI 
       45.07        29.98        19.79        14.53        19.33        50.24 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
       17.79         2.56        19.20        98.33        17.23        66.15 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG 
       10.42        21.14        14.79        16.47        73.64        50.07 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A442 TCGA-LL-A50Y 
       15.68        52.96        85.35        13.22        29.23        25.05 
TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       14.79        14.50        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
       52.96       131.67        48.46        47.61        11.44         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68        31.79         7.96        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      121.94       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW 
      114.81        92.48       107.93        75.25        98.99       107.93 
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-A0EW 
       80.28       118.45        79.76        74.40        72.00        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-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-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-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       23.77        23.47        60.72        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        42.44        17.19        18.15        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        91.07        29.98        32.75        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         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-A13H TCGA-A7-A26G 
       37.45        35.67        33.11        31.73        29.56        23.74 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SF 
       11.34        10.59        10.29        13.41        14.93        17.92 
TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.72        10.29         9.37         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        17.98        31.00        26.01         1.02        17.03 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
        9.99        10.98         7.99        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
        0.99        38.01        28.96        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 
        0.99       112.08        43.00        40.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
        9.99        12.00        50.04        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-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
        0.99        17.03        38.04        19.23        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       60.92        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
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         7.46         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 
        6.90         0.33         5.36         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        69.83        58.95        44.42 
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-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80       113.62       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
      108.03       102.31        98.27        82.68        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       20.45        97.08        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       15.62        32.52       140.55         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        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-A1AL 
      133.22       134.14       125.16       108.36       101.00        97.68 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       96.00        86.07        93.90        37.81        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       112.77        97.84       105.27       102.84 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        54.21        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       40.54        33.30        38.96        10.59        77.62       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       11.90       275.87       129.57        50.70        65.52       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       233.62        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       263.28       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      282.90       169.51        97.48       188.68        18.35        21.01 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      206.86       129.70        28.27        68.94        58.55       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A409 TCGA-B6-A40B 
      139.17       170.17        37.87        85.35        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       71.15        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       39.16        84.13        32.02        18.21        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       70.88        16.27        15.68        14.30         9.63        81.83 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        63.32        10.78        15.16        63.39        53.26 
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-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-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
       32.91         4.90        35.93        20.12        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       55.63        66.05         7.36        51.39        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       82.85        49.58        17.69        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.08       120.62        33.17        74.73       122.83        33.99 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 
       10.52       110.60        20.88         5.26        21.76         9.44 
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-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.56        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
        0.16        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
       12.95        16.87        16.70         0.03        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J9 
       56.81        13.25        20.58        13.97        13.48        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        55.50        18.90        12.03        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.97        20.09        20.12        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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       16.31        16.64        15.16        43.04         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-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       48.03        16.41        17.06         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        46.59        40.41        28.44        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       34.26        31.96        69.34        18.51        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        25.05        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        11.05        19.56        56.94        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        70.36        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       75.81        28.90       106.75       102.61         8.75        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56        30.61        34.92        38.76        34.29        17.69 
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        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84        18.94        24.82        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        48.23        45.01         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
       40.50         0.69         1.94         7.13        24.56         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        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-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-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-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        31.30        33.21         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        83.34        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-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       13.28        10.62        17.06        15.32        14.70        14.47 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       16.08        15.68         7.46        12.36        19.59        17.49 
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-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       58.62        36.36        28.87        24.72        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-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-A6ZH TCGA-S3-AA0Z 
       86.96         0.16         0.26         9.93        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       13.84        17.39        17.26         3.81        66.84        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.33               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             245.1              282.9 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            27.135             28.270 
[1] "0.3 - 245.1 (27.1)" "0.0 - 282.9 (28.3)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        18       16        0        3        73        46
  12P GAIN WILD-TYPE      71       67        6        3       279       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           0         36          6         18        4
  12P GAIN WILD-TYPE         2        119         21         47       16
                    vv
clus                 STAGE X
  12P GAIN MUTATED         3
  12P GAIN WILD-TYPE      10
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 16                 67
  STAGE IB                  0                  6
  STAGE II                  3                  3
  STAGE IIA                73                279
  STAGE IIB                46                207
  STAGE III                 0                  2
  STAGE IIIA               36                119
  STAGE IIIB                6                 21
  STAGE IIIC               18                 47
  STAGE IV                  4                 16
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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  24   9
  12P GAIN WILD-TYPE 229 479 113  31
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               45                229
  T2              146                479
  T3               24                113
  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   107  63  29  21
  12P GAIN WILD-TYPE 399 295  90  56
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              107                399
  N1               63                295
  N2               29                 90
  N3               21                 56
[1] 4 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   189   5
  12P GAIN WILD-TYPE 700  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    189    5
  12P GAIN WILD-TYPE  700   17
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              189                700
  1                5                 17
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   220   5
  12P GAIN WILD-TYPE 847   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    220    5
  12P GAIN WILD-TYPE  847    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE              220                847
  MALE                  5                  7
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    87 114
  12P GAIN WILD-TYPE 350 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     87  114
  12P GAIN WILD-TYPE  350  433
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                87                350
  YES              114                433
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P GAIN MUTATED                            1                           178
  12P GAIN WILD-TYPE                          0                           590
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P GAIN MUTATED                               27                   2
  12P GAIN WILD-TYPE                            174                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P GAIN MUTATED                       2                                9
  12P GAIN WILD-TYPE                     7                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  12P GAIN MUTATED                    1              4
  12P GAIN WILD-TYPE                 16             42
D23V9, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 178                590
  INFILTRATING LOBULAR CARCINOMA                 27                174
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  4                 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"
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0    10
  12P GAIN WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          42   151
  12P GAIN WILD-TYPE                       139   593
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 50
  BLACK OR AFRICAN AMERICAN                      42                139
  WHITE                                         151                593
[1] 4 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     5 182
  12P GAIN WILD-TYPE  34 692
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  182
  12P GAIN WILD-TYPE   34  692
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              182                692
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   157  27
  12Q GAIN WILD-TYPE 760 121
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               184                881 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                27                121 
$`12Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A06T TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09I TCGA-AC-A3W5 
       38.30        53.06        33.01         1.02        45.07        16.57 
TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A5QM TCGA-E2-A15O TCGA-E2-A1L8 
       13.71         5.65        32.91        73.35        50.79        73.64 
TCGA-LL-A740 TCGA-Z7-A8R5 TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04U 
       14.50       108.07        39.32        28.01        18.02        87.25 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       77.19        56.81        67.33        35.05        34.29        31.82 
TCGA-A2-A0SW TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1G1 
       44.88        20.75        21.90        21.67        17.36        19.20 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XW TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J 
       42.44       105.34        56.28        29.79        25.15        20.61 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A8-A06R TCGA-A8-A076 
       14.70        13.74        21.17        14.73        17.98        53.98 
TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08G 
        9.01        10.98         8.98         9.99        45.07        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09N TCGA-A8-A09X 
       37.05        31.00        30.97         9.99         1.02        14.01 
TCGA-A8-A0A1 TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A5XU TCGA-AN-A03Y 
       12.00        22.95         5.72        26.04        14.96         0.33 
TCGA-AN-A0FF TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N 
        5.65         7.04         0.36         0.33        80.28        66.77 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A12E TCGA-AO-A1KQ 
       95.70        32.78        20.32        53.03        70.42        61.87 
TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0U2 TCGA-AR-A1AK TCGA-AR-A1AV 
       11.51        98.33         5.26        83.87       103.86        61.28 
TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
      120.33       104.28       105.30        50.96        98.66        89.00 
TCGA-AR-A2LM TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0X1 
       63.62       165.76       162.05        79.46       113.79       245.10 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B5 TCGA-BH-A0BA 
       43.59        73.51        68.12        62.93        70.22        37.22 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0DD TCGA-BH-A0E7 TCGA-BH-A0EB 
       74.89        77.75        77.95        81.73        44.81        24.49 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L 
       30.35        23.08        27.25        23.05        90.84        26.66 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC 
       37.74        37.55        42.28        12.00        55.69       114.15 
TCGA-BH-A1FM TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12O 
       45.63        23.51         9.63        18.87        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A278 
       12.16        12.49        11.28        12.03        15.45         9.76 
TCGA-D8-A13Z TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1XD 
       20.88        14.17        15.78        18.15        18.90        17.16 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R 
       21.83        12.99        16.54        15.32        13.48        10.09 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O 
       12.26        18.51        34.42        37.51        40.11        44.68 
TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15S TCGA-E2-A1IH 
       32.02        69.96        23.34        18.21        14.07        33.73 
TCGA-E2-A1II TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       33.70        43.04         8.28        22.29        34.16        36.20 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A22D 
       35.24         9.86        11.15        32.09        40.24        41.03 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-EW-A1J6 TCGA-EW-A1OW 
       38.99        12.33        29.72        23.84        28.77        22.82 
TCGA-EW-A1P5 TCGA-EW-A2FV TCGA-GM-A2DI TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A7W5 
       23.11        25.91        85.15         2.60        21.24         7.10 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A66O 
       15.32        22.26         2.63        19.53        34.92        17.36 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-UL-AAZ6 
       18.81        18.48        19.27        17.03 

$`12Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       21.73        22.32        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E 
       19.99        15.06        33.01        33.01        17.95        49.05 
TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT 
       29.98        19.79        14.53        19.33        50.24        17.79 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
        2.56        19.20        98.33        17.23        66.15        57.27 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1LG TCGA-E2-A2P5 
       10.42        21.14        14.79        16.47        50.07        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       29.23        25.05        14.79        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       11.41        52.96       133.05       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A04W 
       18.21       143.15        78.41       121.94        73.84       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 
      107.93        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-A0EW TCGA-A2-A0EX 
      118.45        79.76        74.40        72.00        61.94        24.72 
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-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YI 
       18.90        32.55        25.28        18.21        50.47        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-A1G6 TCGA-A2-A259 TCGA-A2-A25C 
       60.72        22.45        20.25        16.47        52.47        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        47.31        35.93        50.37        50.83 
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-A13H TCGA-A7-A26G 
       35.67        33.11        31.73        20.19        29.56        23.74 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SD 
       11.34        10.59        10.29        13.41        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       17.92        12.10        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02        13.02         1.02        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        1.02        17.03        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A082 
       12.00        32.05         9.99         7.99        24.99        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I 
       36.95        13.02         0.99        38.01        28.96        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-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       41.98        12.00         9.99        12.00        50.04        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 
       25.02         8.98        19.04        15.02         0.99        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-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       19.23        73.91        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79        29.26        16.80        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 
        7.46         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        7.96         7.00         7.59         7.17         6.90         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         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        69.83        58.95        44.42 
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-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F 
      106.78       108.03       102.31        98.27        82.68        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       53.88        40.57        20.45        97.08        82.62        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TS 
       26.93       130.09        15.62        32.52       140.55        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      101.00        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        94.29        86.53        86.43        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       50.89        94.22        99.78       118.59         2.76       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 
       97.84       105.27       102.84        98.76        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       54.21        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       127.33        84.59       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.01       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.55       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        85.35        74.99        18.84       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        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.55        39.16        84.13        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 
       74.14        76.60        85.87        49.94        74.14        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       46.39        89.06        90.97        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
       14.30         9.63        81.83        31.00        63.32        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        63.39        53.26        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        32.91         4.90        35.93        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        97.48        25.08       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8G0 
       10.52       110.60        20.88        18.64         5.26        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.77        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.59        12.92        12.46        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.34         0.16        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36        12.95        16.87        16.70         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        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        56.81        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        19.20        17.49        16.50        55.50 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        53.00        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-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15        12.39        15.22        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       16.64        15.16        43.04        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-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       48.03        16.41        17.06         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        46.59        40.41        28.44        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       34.26        31.96        69.34        18.51        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        25.05        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        11.05        19.56        56.94        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       77.65        37.41        70.36        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90       106.75       102.61         8.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56        30.61        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC 
       17.69        34.82        32.88        36.82        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 
       41.62        35.77        25.84        18.94        24.82        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        48.23        45.01 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.72        40.73        40.50        20.12         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        7.13        24.56         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       13.25        16.57        25.94        29.95        29.85        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-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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        17.52        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        83.34        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-A3XL 
      106.06       101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN 
       11.57        13.28        10.62        32.75        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.47        16.08        15.68         7.46        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       31.99        58.62        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-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       26.04        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-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S 
       21.07        20.68        13.84        17.39        17.26         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        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 
             245.1              282.9 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             26.35              28.44 
[1] "0.3 - 245.1 (26.4)" "0.0 - 282.9 (28.4)"
[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        54        40
  12Q GAIN WILD-TYPE      75       71        6        5       298       213
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           0         36          6         16        4
  12Q GAIN WILD-TYPE         2        119         21         49       16
                    vv
clus                 STAGE X
  12Q GAIN MUTATED         2
  12Q GAIN WILD-TYPE      11
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  14                 75
  STAGE IA                 12                 71
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                54                298
  STAGE IIB                40                213
  STAGE III                 0                  2
  STAGE IIIA               36                119
  STAGE IIIB                6                 21
  STAGE IIIC               16                 49
  STAGE IV                  4                 16
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    35 120  22   9
  12Q GAIN WILD-TYPE 239 505 115  31
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               35                239
  T2              120                505
  T3               22                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
  12Q GAIN MUTATED    74  59  28  19
  12Q GAIN WILD-TYPE 432 299  91  58
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               74                432
  N1               59                299
  N2               28                 91
  N3               19                 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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   158   5
  12Q GAIN WILD-TYPE 731  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    158    5
  12Q GAIN WILD-TYPE  731   17
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              158                731
  1                5                 17
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   181   5
  12Q GAIN WILD-TYPE 886   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    181    5
  12Q GAIN WILD-TYPE  886    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE              181                886
  MALE                  5                  7
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    79  90
  12Q GAIN WILD-TYPE 358 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     79   90
  12Q GAIN WILD-TYPE  358  457
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                79                358
  YES               90                457
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q GAIN MUTATED                            0                           146
  12Q GAIN WILD-TYPE                          1                           622
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q GAIN MUTATED                               25                   1
  12Q GAIN WILD-TYPE                            176                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q GAIN MUTATED                       0                                9
  12Q GAIN WILD-TYPE                     9                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  12Q GAIN MUTATED                    1              3
  12Q GAIN WILD-TYPE                 16             43
D24V9, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 146                622
  INFILTRATING LOBULAR CARCINOMA                 25                176
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  3                 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"
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   122
  12Q GAIN WILD-TYPE                       148   622
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                148
  WHITE                                         122                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"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3 148
  12Q GAIN WILD-TYPE  36 726
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3  148
  12Q GAIN WILD-TYPE   36  726
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO              148                726
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    79  13
  13Q GAIN WILD-TYPE 838 135
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                973 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                135 
$`13Q GAIN MUTATED`
TCGA-A7-A26F TCGA-A8-A091 TCGA-A8-A09C TCGA-AR-A2LR TCGA-A1-A0SK TCGA-A2-A04T 
       24.26        33.01         1.02        57.27        31.79        73.84 
TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A7-A0DA 
       35.05        63.29        18.61        17.36        19.20        35.67 
TCGA-A7-A3J0 TCGA-A8-A07R TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A095 TCGA-A8-A097 
       10.29         8.98        19.96        37.05        41.98        12.00 
TCGA-AC-A2FM TCGA-AC-A5XU TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AS TCGA-AN-A0FT 
       26.04        14.96         0.33         0.23         0.33         7.04 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03U TCGA-AO-A0J7 TCGA-AO-A0JB 
        0.36         0.33        12.33        58.95        20.32        50.70 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AR-A0TT TCGA-AR-A0U3 TCGA-AR-A24U 
      102.31        98.27        82.68       109.02       134.14       102.84 
TCGA-AR-A250 TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0WY 
       89.00       165.76       255.68       162.05       100.70       113.79 
TCGA-BH-A0B9 TCGA-BH-A0BT TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18N 
       51.68        77.75        14.30        24.49        36.85        37.74 
TCGA-BH-A18V TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5IZ TCGA-BH-A6R9 
       51.16        49.58        72.07        57.83        18.64         5.26 
TCGA-C8-A12L TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A1JF 
       11.93        13.51        12.59         0.03        20.58        12.03 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A14T TCGA-E2-A14X 
       15.22        21.83        10.09        12.26        75.98        31.96 
TCGA-E2-A14Y TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A1BD TCGA-E2-A1L9 TCGA-E2-A1LH 
       69.34        19.43        20.71        37.25        19.66       106.75 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RF 
       38.76        34.16        41.62        35.24         2.56         6.58 
TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P7 TCGA-EW-A2FV TCGA-EW-A423 
        1.94         0.79        28.77        30.08        25.91        17.52 
TCGA-EW-A6SA TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-MS-A51U 
       16.77        11.57         7.10         2.63        15.68        22.39 
TCGA-S3-A6ZG TCGA-UU-A93S 
       18.48         3.81 

$`13Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H 
       19.56       107.70        38.30        23.61        31.36        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 
       29.03        19.99        15.06        33.01        33.01        17.95 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       49.05        45.07        29.98        16.57        19.79        14.53 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       19.33        13.71        50.24        17.79         5.65         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM 
       32.91        19.20        98.33        17.23        66.15        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
      133.05       131.67        48.46        47.61        11.44         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-A04W 
      143.15        18.02        78.41       121.94        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        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       118.45        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-A1G6 TCGA-A2-A259 
       23.47        60.72        22.45        20.25        16.47        52.47 
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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        91.07        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        30.61        37.45        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.34        10.59        13.41        14.70        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-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-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        17.98        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        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-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       38.01        28.96        12.00         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A099 
        0.99       112.08        43.00        40.01        30.97         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        9.99        12.00        50.04        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-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
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-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         7.46         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 
        6.90         0.33         0.33         0.33         5.36         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        69.83        44.42        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        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       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       70.42        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        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 
      133.22        83.87       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        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       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V 
        2.76       104.28       112.77        97.84       105.27       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        98.76        98.66        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
       18.77       127.33        84.59       129.07       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      212.25       234.28        81.17        78.02       263.28       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.28        89.46       282.90       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.46        18.35        21.01       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.55        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      139.17       170.17        37.87         7.07        85.35        74.99 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       68.12        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        76.60        85.87        49.94        77.95        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        46.39        89.06        90.97        81.73        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       67.10        38.01        29.98        13.91        78.28        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        79.00        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE 
        4.41        15.68         9.63        44.81        81.83        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        12.00        55.69        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        25.08       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 
      122.83        33.99        63.35        55.00        45.63        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       55.50        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 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
       23.51         9.63        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-A12V 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        48.53        12.56        12.16        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       20.25        12.53        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
       16.70         9.76        24.56        14.43        33.99        12.95 
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        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        13.97        14.17        13.48        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        55.50        15.78        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        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-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15        12.39        17.16        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        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        43.04        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-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.53        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        12.66        25.22        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-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       43.33        34.26        32.02        18.51        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       28.50        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI 
       54.18        60.36        24.59        75.81        28.90       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         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        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       22.29        36.20        36.56        39.55        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       18.94         9.86        24.82        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        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        46.65        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.72        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        13.25        16.57        25.94        22.82 
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-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48         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-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 
       52.73        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       24.99        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        70.85        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-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF 
        2.60        62.47        11.84        21.24        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       32.75        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       16.08         7.46        19.53        12.36        19.59        17.49 
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-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-AA14 
       18.81        21.07        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.26        17.03        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.03               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            255.68             282.90 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            23.325             28.440 
[1] "0.0 - 255.7 (23.3)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1"  
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         6        4        0        1        35        17
  13Q GAIN WILD-TYPE      83       79        6        5       317       236
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           0         17          3          5        2
  13Q GAIN WILD-TYPE         2        138         24         60       18
                    vv
clus                 STAGE X
  13Q GAIN MUTATED         2
  13Q GAIN WILD-TYPE      11
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   6                 83
  STAGE IA                  4                 79
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                35                317
  STAGE IIB                17                236
  STAGE III                 0                  2
  STAGE IIIA               17                138
  STAGE IIIB                3                 24
  STAGE IIIC                5                 60
  STAGE IV                  2                 18
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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  61   8   5
  13Q GAIN WILD-TYPE 256 564 129  35
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               18                256
  T2               61                564
  T3                8                129
  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
  13Q GAIN MUTATED    45  27  14   7
  13Q GAIN WILD-TYPE 461 331 105  70
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               45                461
  N1               27                331
  N2               14                105
  N3                7                 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"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    82   2
  13Q GAIN WILD-TYPE 807  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     82    2
  13Q GAIN WILD-TYPE  807   20
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               82                807
  1                2                 20
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    92   1
  13Q GAIN WILD-TYPE 975  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     92    1
  13Q GAIN WILD-TYPE  975   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               92                975
  MALE                  1                 11
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    43  42
  13Q GAIN WILD-TYPE 394 505
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     43   42
  13Q GAIN WILD-TYPE  394  505
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                43                394
  YES               42                505
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q GAIN MUTATED                            0                            75
  13Q GAIN WILD-TYPE                          1                           693
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q GAIN MUTATED                                4                   1
  13Q GAIN WILD-TYPE                            197                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q GAIN MUTATED                       3                                2
  13Q GAIN WILD-TYPE                     6                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  13Q GAIN MUTATED                    2              6
  13Q GAIN WILD-TYPE                 15             40
D25V9, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  75                693
  INFILTRATING LOBULAR CARCINOMA                  4                197
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  6                 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"
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                          14    66
  13Q GAIN WILD-TYPE                       167   678
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                      14                167
  WHITE                                          66                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"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  74
  13Q GAIN WILD-TYPE  33 800
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   74
  13Q GAIN WILD-TYPE   33  800
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 33
  NOT HISPANIC OR LATINO               74                800
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED   125  18
  14Q GAIN WILD-TYPE 792 130
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                922 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                130 
$`14Q GAIN MUTATED`
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09C TCGA-AC-A5EI TCGA-AR-A5QM TCGA-D8-A146 
       33.01        33.01         1.02        14.53        73.35        21.14 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-A2-A0D2 TCGA-A2-A0T3 TCGA-A2-A0YH 
       50.07        26.99        52.96        33.76        49.84        21.67 
TCGA-A2-A1FW TCGA-A2-A25C TCGA-A2-A3KD TCGA-A2-A4RX TCGA-A7-A0CJ TCGA-A7-A0DB 
       17.36        17.19        39.65        24.39        30.61        33.11 
TCGA-A7-A56D TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A092 
       14.73        17.03        53.98        38.01        12.00        30.97 
TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 
       41.98         9.99        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        22.95        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       120.33       112.77 
TCGA-AR-A250 TCGA-AR-A2LK TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0RO TCGA-B6-A0RS 
       89.00        54.21       281.29       129.57       162.05       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KN TCGA-B6-A401 
      282.90        79.46       113.79       206.86       139.17        85.35 
TCGA-B6-A408 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0DG 
       68.12        37.22        74.89        75.48        77.75        67.10 
TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0HI TCGA-BH-A0HX 
       78.28         2.56        81.83        31.00        20.38        27.25 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1FM 
       44.81        90.84        26.66        69.93        12.00        45.63 
TCGA-BH-A1FU TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W 
       55.50        23.51         5.26        12.66        11.77        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A27A TCGA-D8-A13Z 
       12.16        12.59        12.49        11.28        24.56        20.88 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK 
       20.58        14.17        14.17        18.15        12.03        20.12 
TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XZ TCGA-D8-A27W TCGA-D8-A3Z6 
       18.58        15.22        19.92        15.32        12.26        18.51 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       46.59        40.11        40.96        69.96        23.24        19.43 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A1L9 TCGA-E2-A1LL 
       20.71        18.21        55.63         9.04        19.66        43.04 
TCGA-E2-A9RU TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
       17.69        35.24         9.86        40.24        46.65         6.58 
TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 
       46.59        41.03        41.72         0.69        38.99        12.33 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1OZ TCGA-EW-A1PG TCGA-EW-A2FS 
        0.79        26.40         8.48        40.41        34.55        52.73 
TCGA-EW-A6SA TCGA-GM-A2DB TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-MS-A51U 
       16.77        79.10        15.32        14.47         2.63        22.39 
TCGA-OL-A5RW TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-WT-AB44 TCGA-Z7-A8R6 
       36.36        40.11        18.48        29.03       107.05 

$`14Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A093 
       53.06        29.03        19.99        15.06        33.01        17.95 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS 
       49.05        45.07        29.98        16.57        19.79        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       13.71        50.24        17.79         5.65         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0B6 
       19.20        98.33        17.23        66.15        57.27        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-EW-A1J5 TCGA-GM-A2DD 
       14.79        50.79        16.47        73.64        15.68        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       24.79       114.81        92.48       107.93        77.19        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       118.45 
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-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-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-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D 
       20.25        19.20        16.47        52.47        42.44        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
      105.34        10.59        36.23        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-A0DA TCGA-A7-A0DC 
       35.31        34.29        35.47        37.45        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
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-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        17.92        12.10        10.72 
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-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 
        1.02        17.98        31.00        26.01         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       45.07        18.05        36.95        13.02         0.99        28.96 
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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
      112.08        43.00        40.01        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       50.04         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        13.02        21.04         0.99        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       19.23        73.91         5.72        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       40.57        86.66        90.71        60.92        87.12        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       33.04        19.33        14.66        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        29.26        16.80        14.96        11.44 
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-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-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         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         7.46         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-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        6.90         7.04         0.33         0.33         0.33         5.36 
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-A03M TCGA-AO-A03R TCGA-AO-A03T 
        0.33         5.33         5.59        61.35        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        44.42        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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 
       65.10        26.24        62.04        55.33       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03       102.31        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       70.42        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        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       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O 
       86.43        33.73       160.90        94.22        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       104.28        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        98.76        98.66        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       71.05        93.83       166.42        20.25        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       143.38        11.90       275.87        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       263.28       102.77       140.28 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       169.51        97.48       188.68        18.35        21.01 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 
      101.52        73.51       170.17        37.87         7.07        74.99 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       18.84       103.63        71.15        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        63.09        81.44        39.55        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       84.13        51.68        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       21.70        61.68        72.23        74.14        76.60        85.87 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        81.73        77.98        38.01        29.98        13.91 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         3.22        79.00        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB 
        4.41        15.68        14.30         9.63        44.81        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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-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-A0WA TCGA-BH-A18F 
        5.59        23.93        24.95        42.35        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        4.90        35.93        20.12        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-A1EW TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        97.48        25.08       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       122.83        33.99        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07        53.98        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A8FZ 
       10.52       110.60        20.88        18.64         9.63        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.92        12.46        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A142 
       12.49        13.41        19.46        56.81        13.25        13.97 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        55.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL 
       18.90        53.00        14.01        18.97        20.09        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-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-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM 
       12.39        17.16        14.73        21.83        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       55.30        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        43.04        16.54        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 
       48.03        16.41        13.48        17.06         1.61        10.09 
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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       25.22        43.00        34.42        27.52        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        44.68        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       69.34        18.51        63.62        21.04        23.87        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        53.92 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       54.18        60.36        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      102.61         8.75        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        38.76        34.29        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       22.29        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84        18.94        24.82        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        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       32.09         1.12        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H 
       42.25        37.74        39.09        38.37        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
       20.12         1.94         7.13        24.56        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       26.70        25.81        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.95        29.85        41.13        39.78        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-A1PH TCGA-EW-A2FR TCGA-EW-A2FV 
       13.94        10.52        14.43        19.96        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       24.99        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FR 
       10.62        32.75        17.06        14.70        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68         7.46        19.53        12.36        19.59        17.49 
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-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-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        28.21        19.73         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        18.81        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       20.68        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A 
        3.81        66.84        15.35        16.04 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.33               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            282.90             275.87 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            29.030             28.175 
[1] "0.3 - 282.9 (29.0)" "0.0 - 275.9 (28.2)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         9        8        2        2        45        29
  14Q GAIN WILD-TYPE      80       75        4        4       307       224
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           1         27          5         10        1
  14Q GAIN WILD-TYPE         1        128         22         55       19
                    vv
clus                 STAGE X
  14Q GAIN MUTATED         2
  14Q GAIN WILD-TYPE      11
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  8                 75
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA                45                307
  STAGE IIB                29                224
  STAGE III                 1                  1
  STAGE IIIA               27                128
  STAGE IIIB                5                 22
  STAGE IIIC               10                 55
  STAGE IV                  1                 19
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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  93  15   6
  14Q GAIN WILD-TYPE 245 532 122  34
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               29                245
  T2               93                532
  T3               15                122
  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
  14Q GAIN MUTATED    60  45  24  11
  14Q GAIN WILD-TYPE 446 313  95  66
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               60                446
  N1               45                313
  N2               24                 95
  N3               11                 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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   122   1
  14Q GAIN WILD-TYPE 767  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    122    1
  14Q GAIN WILD-TYPE  767   21
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0              122                767
  1                1                 21
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   142   1
  14Q GAIN WILD-TYPE 925  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    142    1
  14Q GAIN WILD-TYPE  925   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE              142                925
  MALE                  1                 11
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    54  79
  14Q GAIN WILD-TYPE 383 468
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     54   79
  14Q GAIN WILD-TYPE  383  468
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                54                383
  YES               79                468
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q GAIN MUTATED                            0                           110
  14Q GAIN WILD-TYPE                          1                           658
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q GAIN MUTATED                               15                   0
  14Q GAIN WILD-TYPE                            186                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q GAIN MUTATED                       3                                8
  14Q GAIN WILD-TYPE                     6                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  14Q GAIN MUTATED                    2              5
  14Q GAIN WILD-TYPE                 15             41
D26V9, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 110                658
  INFILTRATING LOBULAR CARCINOMA                 15                186
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 22
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  5                 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"
D26V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0    10
  14Q GAIN WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          23    94
  14Q GAIN WILD-TYPE                       158   650
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 50
  BLACK OR AFRICAN AMERICAN                      23                158
  WHITE                                          94                650
[1] 4 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     2 117
  14Q GAIN WILD-TYPE  37 757
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  117
  14Q GAIN WILD-TYPE   37  757
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 37
  NOT HISPANIC OR LATINO              117                757
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    76  11
  15Q GAIN WILD-TYPE 841 137
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                87                978 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                137 
$`15Q GAIN MUTATED`
TCGA-A2-A1G4 TCGA-A8-A09E TCGA-A8-A09K TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN 
       19.56        49.05        29.98       133.05        48.10        39.32 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0T2 TCGA-A2-A1FW 
       98.99        67.33        33.76        31.82         8.38        17.36 
TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XY TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A13F 
       17.19        91.07        35.93        35.31        37.45        25.15 
TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A4SE TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A07P 
       23.74        11.34        21.17        13.02         1.02        10.98 
TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A097 TCGA-A8-A09M TCGA-AC-A2QH 
       24.99        38.01        31.00        12.00        33.07        33.04 
TCGA-AN-A0XU TCGA-AO-A0J2 TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A12D TCGA-AQ-A04L 
        0.33        32.78        71.80       115.27        82.68       130.09 
TCGA-AR-A0TP TCGA-AR-A0U2 TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A254 
      140.55        83.87        61.28        86.43        50.89        85.64 
TCGA-AR-A2LH TCGA-B6-A0I5 TCGA-B6-A0IM TCGA-B6-A400 TCGA-BH-A0BG TCGA-BH-A0BP 
       20.25       281.29       127.33         7.07        61.51        75.48 
TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18V 
       78.28         2.56        31.00        23.05        37.74        51.16 
TCGA-BH-A1FH TCGA-BH-A5J0 TCGA-C8-A12O TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HM 
       33.99        23.51        12.66        12.59        11.28        12.33 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-D8-A1JP TCGA-D8-A27R TCGA-E2-A10A TCGA-E2-A15D 
       12.36        15.45        21.01        10.09        40.41        17.29 
TCGA-E2-A15E TCGA-E2-A1IL TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A56Z 
       20.71         3.88        28.90       106.75        43.04         8.28 
TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A54X TCGA-EW-A1IY 
       34.16        35.24         2.56        45.01        23.90         8.48 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GM-A2DF TCGA-GM-A2DK 
       28.77        22.82        23.11        19.99        70.85        86.96 
TCGA-LL-A5YM TCGA-OL-A5RV TCGA-PL-A8LX 
       15.32        34.92         0.16 

$`15Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
      107.70        38.30        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       17.95         1.02        45.07        16.57        19.79        14.53 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       19.33        13.71        50.24        17.79         5.65         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
       32.91        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
      108.07       131.67        48.46        47.61        11.44         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68        31.79         7.96        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       18.02        78.41       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19        75.25         5.19       107.93        56.81 
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 
      118.45        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-A25B 
       22.45        20.25        19.20        16.47        52.47        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        36.23        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        56.28        47.31        50.37        50.83 
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-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       21.90        34.29        35.47        30.61        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IZ 
       29.79        31.73        20.19        29.56        20.61        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.29        13.41        14.70        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       10.42         8.75        13.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        17.03        53.98         9.01        43.00        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R 
       18.97        14.01        12.00        32.05         9.99         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        45.07        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
        0.99        28.96        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09N 
       41.98         9.99         9.99        12.00        50.04         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        19.23        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        74.14        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       16.80        14.96        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-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-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 
        7.46         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         6.90 
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 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT 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        69.83        58.95        44.42 
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-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       65.10        26.24        62.04        55.33       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
      106.78       108.03       102.31        98.27        70.42        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       53.88        40.57        20.45        97.08        61.87        82.62 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ 
       11.51        24.79        26.93        15.62        32.52        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        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       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       86.07        93.90        99.32        37.81        94.29        86.53 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28       112.77        97.84       105.27       102.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      105.30        50.96        98.76        98.66        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK 
       93.30        71.05        93.83       166.42        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
       85.35        74.99        68.12        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        84.13        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        43.53        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       72.23        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        74.14        41.75        46.39        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         3.22        79.00        67.86        70.88        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        81.83 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        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        32.91         4.90        35.93        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        97.48        25.08       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       122.83        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        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       110.60        20.88        18.64         9.63         5.26 
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-A12P TCGA-C8-A12Q 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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       48.53        12.56        12.16        13.51        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
       12.46        12.49        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       12.03        12.95        12.33        20.25        12.53        12.95 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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 
       56.81        20.88        13.25        20.58        13.97        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        55.50 
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        53.00        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-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-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        14.73        21.83        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       55.30        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        43.04        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        48.03        16.41        13.48        17.06         1.61 
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        12.66        25.22        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-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        75.98 
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        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       25.05        23.34        22.82        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       56.94        14.07        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN 
       70.36        33.73        33.70        28.44        59.18        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       75.81       102.61         8.75        34.55        43.56        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        22.29        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB 
       34.95         6.12         3.02        11.15        48.23        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       38.37        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        26.70         0.79        25.81        26.40        27.85 
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-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-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC 
       29.82        18.48        30.08         7.86        18.90         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-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        17.52 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       23.51        15.22        16.77        24.99        31.30        33.21 
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-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       72.10        85.15       115.69       106.06       101.62       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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN 
        7.10        13.28        10.62        32.75        17.06        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RW 
        2.10        36.30        58.52        31.99        58.62        36.36 
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-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-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       86.96         0.26         9.93        18.81        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       20.68        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        29.03        15.35        16.04       107.05 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.16               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            281.29             282.90 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            31.000             27.715 
[1] "0.2 - 281.3 (31.0)" "0.0 - 282.9 (27.7)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED        10        6        0        0        30        17
  15Q GAIN WILD-TYPE      79       77        6        6       322       236
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1         13          2          5        3
  15Q GAIN WILD-TYPE         1        142         25         60       17
                    vv
clus                 STAGE X
  15Q GAIN MUTATED         1
  15Q GAIN WILD-TYPE      12
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                  6                 77
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                30                322
  STAGE IIB                17                236
  STAGE III                 1                  1
  STAGE IIIA               13                142
  STAGE IIIB                2                 25
  STAGE IIIC                5                 60
  STAGE IV                  3                 17
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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  49  12   3
  15Q GAIN WILD-TYPE 251 576 125  37
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               23                251
  T2               49                576
  T3               12                125
  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    42  27  10   7
  15Q GAIN WILD-TYPE 464 331 109  70
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               42                464
  N1               27                331
  N2               10                109
  N3                7                 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"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    76   3
  15Q GAIN WILD-TYPE 813  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     76    3
  15Q GAIN WILD-TYPE  813   19
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               76                813
  1                3                 19
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    87   1
  15Q GAIN WILD-TYPE 980  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     87    1
  15Q GAIN WILD-TYPE  980   11
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               87                980
  MALE                  1                 11
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    35  47
  15Q GAIN WILD-TYPE 402 500
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     35   47
  15Q GAIN WILD-TYPE  402  500
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                35                402
  YES               47                500
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q GAIN MUTATED                            0                            76
  15Q GAIN WILD-TYPE                          1                           692
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q GAIN MUTATED                                3                   0
  15Q GAIN WILD-TYPE                            198                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q GAIN MUTATED                       1                                1
  15Q GAIN WILD-TYPE                     8                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  15Q GAIN MUTATED                    2              4
  15Q GAIN WILD-TYPE                 15             42
D27V9, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  76                692
  INFILTRATING LOBULAR CARCINOMA                  3                198
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  4                 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"
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                          16    52
  15Q GAIN WILD-TYPE                       165   692
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                      16                165
  WHITE                                          52                692
[1] 4 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  70
  15Q GAIN WILD-TYPE  36 804
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   70
  15Q GAIN WILD-TYPE   36  804
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO               70                804
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   393  66
  16P GAIN WILD-TYPE 524  82
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               459                606 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                66                 82 
$`16P GAIN MUTATED`
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A426 TCGA-A8-A06U 
       63.12        88.60        31.36        23.80        11.97        29.03 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E 
       15.06        33.01        33.01        33.01        17.95        49.05 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A54O 
       29.98        16.57        19.33        13.71         5.65        32.91 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       66.15        73.35        54.05        32.58        21.44        89.16 
TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 
       21.14        50.79        16.47        73.64        50.07        26.99 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LL-A5YP TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-A1-A0SF 
       52.96        75.02        14.79        11.41       108.07        48.10 
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P 
       14.27        20.88        13.68        28.01       143.15        18.02 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 
       24.79       114.81        92.48        77.19        56.81        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       61.58       101.72        80.28        35.05        34.29        31.82 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       54.64        27.12        44.88        17.13         8.38        49.84 
TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       17.46        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3XX 
       18.61        23.77        17.36        20.25        52.47        47.31 
TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0DB 
       35.93        26.96        21.14        35.31        35.47        33.11 
TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE 
       29.79        29.56        20.61        14.70        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06Q 
       17.92        12.10        10.72        10.42        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J 
       17.98        31.00        26.01         1.02        18.97        12.00 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 
       10.98         8.98         9.99        45.07        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08P 
        0.99        38.01        28.96        19.96        12.00        31.00 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
      112.08        40.01        30.97        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 
       12.00        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        22.95        73.91        22.26 
TCGA-AC-A2FG TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3QQ 
       60.92        74.14        19.33        32.45        22.19        24.13 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AN-A03X 
       14.96        11.44        17.42        18.67         1.68         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ 
        0.33         0.23         0.62         2.96         1.78         9.96 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        0.16         7.00         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L 
        5.36        12.33         0.33         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JE 
       66.77        81.63        44.42        20.32        53.03        76.77 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12A TCGA-AO-A12E 
       55.33        71.80       115.27       113.62       102.31        70.42 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AR-A0TR 
       97.08        61.87        11.51        24.79        15.62         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK 
       84.10        75.22        98.93        83.87       108.36       103.86 
TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L 
       97.68        93.90        37.81        61.28        86.43        94.22 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 
       99.78         2.76       104.28        98.76        89.00        85.64 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A5QP TCGA-B6-A0I2 
       71.05        54.21        63.62        39.39        38.96       143.38 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0IP 
      129.57        65.52       146.50       112.37       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      140.88       234.28        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ 
      140.28       100.70        97.48       188.68       113.79       206.86 
TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
      245.10       101.52        73.51        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 
       71.15        62.93        59.84        20.45        25.55        39.55 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BQ 
       70.22        37.22        61.51        74.89        75.48        74.14 
TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DL TCGA-BH-A0DP 
       77.75        46.39        89.06        90.97        78.28        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E6 
        2.56        79.00        67.86        70.88        16.27         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H3 
       44.81        81.83        24.49        31.00        30.35        63.39 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
       24.56        41.00        20.38        36.85        12.89        27.25 
TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I 
       23.93        42.35        44.81        23.05        32.91        35.93 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V 
       26.66        72.56        37.74        55.63         7.36        51.16 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FG 
       91.99        12.00        49.58        31.53       120.62       122.83 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A42V 
       45.63        72.07        26.14        83.31        57.83        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
       23.51         9.63        11.93        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 
       12.66        48.53        12.56        13.51        12.59        12.49 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W 
       11.34        11.28        12.03        12.33        12.95        12.53 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A141 
       12.95        15.45        16.70        13.02        20.88        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD 
       13.97        14.17        13.48        14.17        17.49        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 
       18.90        12.03        53.00        20.09        20.12        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       17.79        16.73        27.58        18.15        12.39        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW 
       21.83        19.92        15.85        16.31        12.99        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27K 
       16.54        15.32         9.93        14.24        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A73X TCGA-E2-A107 
       16.41        12.26        33.37        18.51        25.22        34.42 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q 
       40.41        37.51        40.11        28.87        44.68        38.24 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 
       43.33        34.26        31.96        18.51        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       19.43        23.87        22.82        17.29        20.71        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B5 
       55.63        53.92         9.04        11.05        53.62        32.35 
TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L9 
       37.25        37.41        28.44        60.99        11.08        19.66 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N5 TCGA-E9-A1N8 
       43.04        34.55         8.28        30.61        36.82        34.16 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 
       35.24        25.84         9.86        24.82        28.27         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        46.65        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 
       34.45        38.37        41.72        40.50        38.99         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FL 
       24.56        12.33        29.72        32.91        30.44         0.79 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       26.40        27.85         8.48        16.57        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PG TCGA-EW-A2FS 
       40.41        29.82        23.11        18.48        34.55        52.73 
TCGA-EW-A3E8 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       34.03        16.77        31.30        33.21         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A3XN TCGA-GM-A5PV 
      216.76        79.10        85.15       101.62        66.38        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FP 
       18.12        11.57        21.24        17.06        15.32        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        2.63        15.68        19.53        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66K 
        2.10        31.99        34.92        28.87        22.32        41.92 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       26.04        19.73        86.96         9.93        18.48        21.07 
TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-Z7-A8R6 
       17.03        66.84       107.05 

$`16P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A2-A25A 
       48.56        48.36        19.20        36.13        19.56       107.70 
TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 
       38.30        23.61        24.26        21.73        22.32        11.28 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A09C TCGA-A8-A09I TCGA-AC-A3W6 
       11.05        53.06        19.99         1.02        45.07        19.79 
TCGA-AC-A5EI TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM 
       14.53        50.24        17.79         2.56        19.20        98.33 
TCGA-AR-A1AR TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A158 
       17.23        57.27        81.63         9.70        10.42        14.79 
TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       15.68        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AAAU 
       14.50        40.08        18.87        13.94        52.96       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.37        43.43        47.24        31.79         7.96        39.32 
TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       18.21        78.41       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
       55.43       136.73        99.12       107.93        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN 
       98.99       107.93        67.33        34.55        25.22       134.40 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        79.76        74.40        72.00        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 
       63.29        99.19        50.43        44.28        17.52        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       18.90        20.75        32.55        49.48        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 
       31.73        23.47        60.72        22.45        19.20        16.47 
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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        91.07        29.98        32.75        56.28 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       21.90        34.29        30.61        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       20.19        25.15        23.74        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW 
       13.41        14.93        14.50        14.73        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
        8.75        13.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U 
       18.97        14.01        32.05         9.99         7.99        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-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
        9.99        50.04        33.07         1.02        25.02         8.98 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23C TCGA-AC-A23H 
        0.99        19.04        13.02        21.04        19.23         5.72 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FK 
       73.05        99.35        40.57        86.66        90.71        87.12 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        33.04        14.66         6.48        16.31        14.83 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       16.80        13.58        12.26         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AK 
        1.12         1.32         2.30         0.33         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         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-A0FX 
        7.96         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.30         0.33         5.33         5.59        61.35 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
       95.70        68.75        69.83        58.95        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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A126 
       50.86        72.00        65.10        26.24        62.04       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
      106.78       108.03        98.27        82.68        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 
       40.57        20.45        82.62        26.93       130.09        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      140.55        98.33       109.02        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       133.22       134.14       107.21       125.16       101.00 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       96.00        86.07        99.32        94.29        86.53        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24R TCGA-AR-A24S 
      160.90        50.89       120.33       118.59       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 
      105.27       102.84       105.30        50.96        98.66        99.62 
TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LN 
       93.30        93.83       166.42        20.25        86.53        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 
       40.54        33.30        10.59        77.62       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      275.87        50.70       233.62        18.77       127.33        84.59 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RT TCGA-B6-A0RU 
      255.68        68.45       212.25        81.17        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X4 
      169.51        79.46        18.35        21.01       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.55        43.59       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
        7.07        74.99        18.84        63.09        81.44        39.16 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       84.13        51.68        32.02        18.21        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       61.68        72.23        76.60        85.87        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       74.14        41.75        81.73        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       29.98        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 
       63.32        10.78        15.16        53.26        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         4.90        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        25.08 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        33.17        74.73        33.99        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O 
       53.98        55.50        28.14        38.60       130.16        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A6R9 
       36.79        20.12        10.52       110.60        18.64         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66        12.66        12.16        12.59        12.92        12.46 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X 
       12.33        10.92         0.16        12.33        20.25        12.36 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       16.87         0.03         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JH TCGA-D8-A1JI 
       19.20        16.50        55.50        15.78        14.01        18.97 
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-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       14.70        25.74        23.90        17.16        14.73        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 
       17.69        55.30        16.41        16.64        15.16        15.52 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M 
       14.14        17.42        16.04        13.45        13.05        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A4Z1 
       17.06         1.61        10.09        13.08        12.53        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10E 
       16.18        12.66        43.00        27.52        46.59        28.44 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W 
       47.15        40.96        38.60        33.17        75.98        32.02 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F 
       69.34        63.62        21.04        25.05        23.34        21.63 
TCGA-E2-A15H TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       12.92        20.58        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG 
       76.57        87.22        33.01        28.50        77.65        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 
       33.73        33.70        59.18         3.88        22.19        54.18 
TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       60.36        24.59        75.81        28.90       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.75        43.56        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.82        32.88        22.29        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NH TCGA-E9-A1R2 TCGA-E9-A1RF TCGA-E9-A227 
       41.62        35.77        18.94        34.95         6.58        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A243 
       42.25        37.74        39.09        41.03        40.73        20.12 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54X 
        0.69         1.94         9.47        38.07        30.18        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       23.84        26.70        25.81        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       18.90        13.25        28.77        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       39.78        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV 
       13.94        10.52        14.43        19.96        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB 
       22.09        17.49        17.52        23.51        15.22        24.99 
TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       59.57        83.34        70.85        72.10        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 
      106.06       110.50        38.20        43.73        69.30        72.03 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
        2.60        62.47        11.84         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7T0 
       32.75        14.70        14.47        16.08         7.46        12.36 
TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RY 
       19.59        36.30        58.52        58.62        36.36        24.72 
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-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        28.21        40.11         8.91        47.01        64.21 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26        18.81        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.39        17.26         3.81        29.03        15.35        16.04 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.16               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            263.28             282.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            28.270             28.175 
[1] "0.2 - 263.3 (28.3)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED        42       34        3        5       142       112
  16P GAIN WILD-TYPE      47       49        3        1       210       141
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           1         68         15         24        8
  16P GAIN WILD-TYPE         1         87         12         41       12
                    vv
clus                 STAGE X
  16P GAIN MUTATED         4
  16P GAIN WILD-TYPE       9
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  42                 47
  STAGE IA                 34                 49
  STAGE IB                  3                  3
  STAGE II                  5                  1
  STAGE IIA               142                210
  STAGE IIB               112                141
  STAGE III                 1                  1
  STAGE IIIA               68                 87
  STAGE IIIB               15                 12
  STAGE IIIC               24                 41
  STAGE IV                  8                 12
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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   115 266  62  18
  16P GAIN WILD-TYPE 159 359  75  22
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              115                159
  T2              266                359
  T3               62                 75
  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   217 152  56  28
  16P GAIN WILD-TYPE 289 206  63  49
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0              217                289
  N1              152                206
  N2               56                 63
  N3               28                 49
[1] 4 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   385   9
  16P GAIN WILD-TYPE 504  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    385    9
  16P GAIN WILD-TYPE  504   13
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              385                504
  1                9                 13
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   455   7
  16P GAIN WILD-TYPE 612   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    455    7
  16P GAIN WILD-TYPE  612    5
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE              455                612
  MALE                  7                  5
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   186 239
  16P GAIN WILD-TYPE 251 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    186  239
  16P GAIN WILD-TYPE  251  308
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               186                251
  YES              239                308
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P GAIN MUTATED                            1                           340
  16P GAIN WILD-TYPE                          0                           428
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P GAIN MUTATED                               86                   2
  16P GAIN WILD-TYPE                            115                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P GAIN MUTATED                       3                               16
  16P GAIN WILD-TYPE                     6                               14
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  16P GAIN MUTATED                    2             11
  16P GAIN WILD-TYPE                 15             35
D28V9, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 340                428
  INFILTRATING LOBULAR CARCINOMA                 86                115
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)               16                 14
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                 11                 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"
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1    24
  16P GAIN WILD-TYPE                                0    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          62   324
  16P GAIN WILD-TYPE                       119   420
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          24                 36
  BLACK OR AFRICAN AMERICAN                      62                119
  WHITE                                         324                420
[1] 4 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    11 368
  16P GAIN WILD-TYPE  28 506
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11  368
  16P GAIN WILD-TYPE   28  506
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 28
  NOT HISPANIC OR LATINO              368                506
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   113  28
  16Q GAIN WILD-TYPE 804 120
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               141                924 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                28                120 
$`16Q GAIN MUTATED`
TCGA-A7-A426 TCGA-A8-A08F TCGA-AQ-A54O TCGA-GM-A2DD TCGA-LL-A5YP TCGA-A1-A0SG 
       11.97        33.01        32.91        75.02        14.79        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A04P TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0D2 
       20.88        13.68        18.02        24.79        56.81        33.76 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YF TCGA-A2-A0YG 
       35.05        31.82        27.12        44.88        50.47        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        35.93        26.96        29.79 
TCGA-A7-A425 TCGA-A7-A5ZV TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07W TCGA-A8-A08I 
       14.70        12.10        26.01         1.02         9.99        12.00 
TCGA-A8-A0A7 TCGA-AC-A3BB TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A041 TCGA-AN-A049 
        0.99        32.45        11.44        17.42         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AO-A0JE TCGA-AO-A0JL 
        2.96         9.96         0.33        12.33        76.77        55.33 
TCGA-AO-A1KQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A1AX 
       61.87         5.26        84.10        98.93        61.28        86.43 
TCGA-AR-A24L TCGA-AR-A250 TCGA-AR-A255 TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RM 
       94.22        89.00        71.05        65.52       165.76        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WT 
      263.28       162.05       102.77       140.28       100.70       188.68 
TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A409 TCGA-BH-A0BG 
      113.79       101.52        73.51        85.35        18.84        61.51 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0C7 TCGA-BH-A0DL TCGA-BH-A0DX TCGA-BH-A0H6 
       74.89        77.75        90.97        78.28        70.88        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q 
       23.08        41.00        35.93        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        13.51        12.59        12.03 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A8HP TCGA-D8-A142 TCGA-D8-A143 
       12.33        12.95        15.45        13.02        13.97        14.17 
TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ 
       12.03        20.12        16.73        18.15        15.22        21.83 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27W 
       12.99        43.04        15.32        14.24        14.43        12.26 
TCGA-D8-A73X TCGA-E2-A10F TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15M 
       25.22        28.87        31.96        69.96        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-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 
       38.37        38.99         0.79        22.82        29.82        23.11 
TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A3XN TCGA-LL-A5YM TCGA-LL-A6FQ 
      109.87       216.76        79.10        66.38        15.32         2.63 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-PE-A5DE TCGA-PL-A8LZ 
       15.68        19.53         2.10        22.32        86.96         9.93 
TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-V7-A7HQ 
       21.07        17.03        66.84 

$`16Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        21.73        22.32        11.28        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       29.03        19.99        15.06        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
        1.02        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       14.53        19.33        13.71        50.24        17.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
        2.56        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO 
       73.64        50.07        26.99        15.68        52.96        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU 
       13.22        24.95        29.23        25.05        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU 
       18.87        13.94        11.41        52.96       108.07       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
       14.37        43.43        48.10        47.24        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
       39.32        28.01        18.21       143.15        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48       107.93        77.19        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       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       72.00        34.29        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        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-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       25.28        18.21        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-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.20        16.47        52.47        42.44        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        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        32.75        56.28        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       24.39        21.30        23.21        21.14        21.90        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-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB 
       11.34        10.59        10.29        13.41        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VV 
       14.50        21.17        17.92        14.73        10.72        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-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        31.00        17.03        53.98         9.01        43.00 
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-A07Z TCGA-A8-A082 
       10.98         8.98         7.99        24.99        45.07        18.05 
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-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       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-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        9.99        12.00        50.04        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 
       19.23        22.95        73.91         5.72        22.26        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH 
       26.04        74.14        33.04        19.33        14.66         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
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-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-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         1.78         1.71         7.36         7.46         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-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP 
        0.36         0.33         0.33         5.36         0.33         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 
       69.83        58.95        44.42        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-A0JJ 
       50.70        50.86        72.00        65.10        26.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      102.31        98.27        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       40.57        20.45        97.08        82.62        11.51        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
      109.02        75.22        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 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      101.00       103.86        97.68        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H 
       99.32        37.81        94.29        86.53        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       50.89       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       98.76        98.66        99.62        93.30        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        11.90       275.87       129.57        50.70 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WV 
       81.17        89.46       282.90       169.51        97.48        79.46 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.01       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.55        43.59       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        74.99        68.12       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        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        43.53        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        76.60        85.87        49.94        77.95        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        46.39        89.06        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       38.01        29.98        13.91        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       79.00        67.86        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        81.83        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HA 
       30.35        10.78        15.16        63.39        53.26        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-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        90.84        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        12.00        55.69        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        25.08       114.15        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU 
       33.99        63.35        55.00        45.63        53.98        55.50 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       28.14        26.14        38.60       130.16        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       110.60        20.88        18.64        23.51 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       48.53        12.56        12.16        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 
       12.95        12.33        20.25        12.53        12.36        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       16.70         0.03         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.25        20.58        13.48        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       16.50        55.50        15.78        18.15        18.90        53.00 
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-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        16.64        15.16        16.54        15.52         9.93 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.14        17.42        16.04        13.45        13.05        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        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        12.66 
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        75.98        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       69.34        18.51        63.62        23.24        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        76.57        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       33.01        28.50        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        33.70        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90       106.75       102.61         8.75        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       18.94        24.82        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-A1RD 
        3.02        11.15        48.23        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       32.05        42.25        37.74        39.09        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12         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        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
       30.18        30.44        23.90        23.84        26.70        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.90        13.25        16.57        28.77        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.85        40.41        41.13        39.78        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-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       110.50        38.20        43.73        69.30 
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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
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-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 
       12.36        19.59        17.49        27.91        22.39        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        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-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-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
       18.81        18.48        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.26         3.81        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 
            263.28             282.90 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             27.12              28.24 
[1] "0.2 - 263.3 (27.1)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED        12        9        0        1        40        33
  16Q GAIN WILD-TYPE      77       74        6        5       312       220
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         27          7          7        4
  16Q GAIN WILD-TYPE         2        128         20         58       16
                    vv
clus                 STAGE X
  16Q GAIN MUTATED         1
  16Q GAIN WILD-TYPE      12
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  12                 77
  STAGE IA                  9                 74
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                40                312
  STAGE IIB                33                220
  STAGE III                 0                  2
  STAGE IIIA               27                128
  STAGE IIIB                7                 20
  STAGE IIIC                7                 58
  STAGE IV                  4                 16
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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    31  82  20   8
  16Q GAIN WILD-TYPE 243 543 117  32
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               31                243
  T2               82                543
  T3               20                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
  16Q GAIN MUTATED    65  42  24   7
  16Q GAIN WILD-TYPE 441 316  95  70
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               65                441
  N1               42                316
  N2               24                 95
  N3                7                 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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   118   4
  16Q GAIN WILD-TYPE 771  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    118    4
  16Q GAIN WILD-TYPE  771   18
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0              118                771
  1                4                 18
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   138   4
  16Q GAIN WILD-TYPE 929   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    138    4
  16Q GAIN WILD-TYPE  929    8
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE              138                929
  MALE                  4                  8
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    57  67
  16Q GAIN WILD-TYPE 380 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     57   67
  16Q GAIN WILD-TYPE  380  480
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                57                380
  YES               67                480
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q GAIN MUTATED                            1                           112
  16Q GAIN WILD-TYPE                          0                           656
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q GAIN MUTATED                               14                   1
  16Q GAIN WILD-TYPE                            187                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q GAIN MUTATED                       3                                5
  16Q GAIN WILD-TYPE                     6                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  16Q GAIN MUTATED                    1              5
  16Q GAIN WILD-TYPE                 16             41
D29V9, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 112                656
  INFILTRATING LOBULAR CARCINOMA                 14                187
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  5                 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"
D29V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     9
  16Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          30    95
  16Q GAIN WILD-TYPE                       151   649
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      30                151
  WHITE                                          95                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"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2 126
  16Q GAIN WILD-TYPE  37 748
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2  126
  16Q GAIN WILD-TYPE   37  748
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 37
  NOT HISPANIC OR LATINO              126                748
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    93  17
  17P GAIN WILD-TYPE 824 131
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               110                955 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                131 
$`17P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A09E TCGA-AR-A2LL TCGA-LL-A5YP TCGA-5T-A9QA TCGA-A1-A0SJ 
       38.30        49.05        66.15        14.79         9.96        13.68 
TCGA-A2-A0CX TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T1 TCGA-A2-A0YJ 
       56.81        35.05        34.29        31.82        17.13        18.61 
TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ 
       23.77        60.72        52.47        29.98        47.31        50.37 
TCGA-A7-A0DC TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A8-A07P TCGA-A8-A08G TCGA-A8-A08J 
       29.79        20.61        10.29        10.98        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A097 TCGA-A8-A09B TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM 
       31.00        12.00        12.00        73.91         5.72        26.04 
TCGA-AC-A2QH TCGA-AC-A5XU TCGA-AC-A8OP TCGA-AN-A04A TCGA-AO-A03L TCGA-AO-A0J5 
       33.04        14.96        20.19         2.96        80.28        26.04 
TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E TCGA-AR-A0TQ 
       20.32        55.33       115.27        98.27        70.42        98.33 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A252 
       61.28        86.53        50.89       104.28       112.77        93.30 
TCGA-AR-A2LK TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX 
       54.21        21.01        43.59       101.52        73.51        37.87 
TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BG TCGA-BH-A0BT 
       85.35        62.93        20.45        39.16        61.51        77.75 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0HQ TCGA-BH-A0HW 
       41.75        89.06        90.97        67.10        36.85        51.32 
TCGA-BH-A18N TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A204 TCGA-C8-A12W 
       37.74        49.58        25.81       114.15        83.31        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-D8-A143 
       12.16        12.59        11.28        12.33        12.95        14.17 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A27W 
       55.50        12.03        20.09        18.15        16.31        12.26 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14W TCGA-E2-A1B1 
       34.42        46.59        44.68        38.60        32.02        87.22 
TCGA-E2-A1B5 TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1QZ TCGA-E9-A1R6 TCGA-E9-A1RH 
       32.35         8.75        38.76        24.82        11.15        46.59 
TCGA-E9-A22E TCGA-E9-A54Y TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A6SA 
       41.72        23.84        29.85         6.15        52.73        16.77 
TCGA-GM-A2DK TCGA-HN-A2NL TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OL-A66K 
       86.96         2.60        15.68        19.53        22.39        41.92 
TCGA-OL-A6VO TCGA-S3-A6ZG 
       28.21        18.48 

$`17P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
       17.95         1.02        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 
       14.53        19.33        13.71        50.24        17.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR 
        2.56        32.91        19.20        98.33        17.23        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 
       85.35        13.22        24.95        29.23        25.05        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB 
      133.05       131.67        48.46        47.61        11.44         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-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       18.02        78.41       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        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       118.45        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-A0T2 TCGA-A2-A0T3 
       44.88        50.43        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-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       18.21        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        31.73        23.47        17.36        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       19.20        16.47        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        36.23        39.65        33.93        91.07        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        35.93        50.83         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-A13D 
       35.47        30.61        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        25.15        29.56        23.74        11.34        10.59 
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-A6VV TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        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-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-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99         8.98         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-A08I TCGA-A8-A08L TCGA-A8-A08O 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-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       40.01        30.97        41.98         9.99         9.99        50.04 
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        19.23        22.95 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       60.92        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
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-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03         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-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         7.46         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-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         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         5.36         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-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       58.95        44.42        32.78        21.40        52.18        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-A0JM TCGA-AO-A125 
       76.77        65.10        26.24        62.04        71.80       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
      108.72       106.78       108.03       102.31        82.68        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       53.88        40.57        20.45        97.08        61.87        82.62 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       11.51        24.79        26.93       130.09        15.62        32.52 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      140.55         5.26        84.10       109.02        75.22        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       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       94.29        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59         2.76        97.84       105.27       102.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      105.30        50.96        98.76        98.66        89.00        99.62 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 
       58.55       139.17       170.17         7.07        74.99        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       18.84       103.63        71.15        59.84        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       81.44        39.55        70.22        84.13        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        43.53        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       72.23        75.48        74.14        76.60        85.87        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       77.95        74.14        46.39        81.73        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        81.83        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        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 
       32.91         4.90        35.93        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-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-A1EY TCGA-BH-A1F2 TCGA-BH-A1F6 
       42.28        12.00        55.69        17.69        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.08       120.62        33.17        74.73       122.83        33.99 
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        53.98        55.50 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        26.14        38.60        57.83       130.16        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       36.79        20.12        10.52       110.60        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92        12.46        12.49        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       11.34         0.16        12.03        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        13.48        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        53.00        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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.64        12.99        15.16        43.04 
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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       25.22        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-A14S 
       28.44        28.87        47.15        40.96        38.24        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        34.26        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       53.62        33.01        28.50        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       24.59        75.81        28.90       106.75       102.61        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
       34.55        43.56         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 
       17.69        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84        18.94         9.86        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        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
        1.12        46.65         6.58        21.27        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.18        30.44        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        28.77        25.94 
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-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        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       85.15       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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.62        32.75        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
       22.26         2.63        16.08         7.46        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       17.49        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        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-A66N 
       20.38        26.70        23.47        65.62        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-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       21.07        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              2.60               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            115.27             282.90 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            34.355             26.990 
[1] "2.6 - 115.3 (34.4)" "0.0 - 282.9 (27.0)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         8        7        0        1        37        26
  17P GAIN WILD-TYPE      81       76        6        5       315       227
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1         19          5          3        3
  17P GAIN WILD-TYPE         1        136         22         62       17
                    vv
clus                 STAGE X
  17P GAIN MUTATED         0
  17P GAIN WILD-TYPE      13
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   8                 81
  STAGE IA                  7                 76
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                37                315
  STAGE IIB                26                227
  STAGE III                 1                  1
  STAGE IIIA               19                136
  STAGE IIIB                5                 22
  STAGE IIIC                3                 62
  STAGE IV                  3                 17
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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    24  60  18   8
  17P GAIN WILD-TYPE 250 565 119  32
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               24                250
  T2               60                565
  T3               18                119
  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
  17P GAIN MUTATED    50  37  17   4
  17P GAIN WILD-TYPE 456 321 102  73
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               50                456
  N1               37                321
  N2               17                102
  N3                4                 73
[1] 4 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    94   3
  17P GAIN WILD-TYPE 795  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     94    3
  17P GAIN WILD-TYPE  795   19
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               94                795
  1                3                 19
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED   105   5
  17P GAIN WILD-TYPE 962   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED    105    5
  17P GAIN WILD-TYPE  962    7
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE              105                962
  MALE                  5                  7
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    34  69
  17P GAIN WILD-TYPE 403 478
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     34   69
  17P GAIN WILD-TYPE  403  478
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                34                403
  YES               69                478
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P GAIN MUTATED                            0                            86
  17P GAIN WILD-TYPE                          1                           682
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P GAIN MUTATED                               11                   1
  17P GAIN WILD-TYPE                            190                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P GAIN MUTATED                       1                                3
  17P GAIN WILD-TYPE                     8                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  17P GAIN MUTATED                    2              6
  17P GAIN WILD-TYPE                 15             40
D30V9, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  86                682
  INFILTRATING LOBULAR CARCINOMA                 11                190
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  6                 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"
D30V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  1     8
  17P GAIN WILD-TYPE                                0    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          23    70
  17P GAIN WILD-TYPE                       158   674
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      23                158
  WHITE                                          70                674
[1] 4 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     3  90
  17P GAIN WILD-TYPE  36 784
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3   90
  17P GAIN WILD-TYPE   36  784
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO               90                784
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   184  34
  17Q GAIN WILD-TYPE 733 114
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               218                847 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                34                114 
$`17Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26H TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S 
       38.30        23.80        22.32        29.03        33.01        33.01 
TCGA-A8-A09E TCGA-AQ-A54O TCGA-AR-A2LL TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-4H-AAAK 
       49.05        32.91        66.15        15.68        52.96        11.44 
TCGA-5T-A9QA TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CU TCGA-A2-A0CX 
        9.96        47.24        13.68       121.94         5.19        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T1 
       33.76        25.22        35.05        34.29        31.82        17.13 
TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A25D 
       49.84        23.77        60.72        20.25        52.47        18.15 
TCGA-A2-A25E TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A7-A0DA TCGA-A7-A0DC 
      105.34        29.98        47.31        50.37        35.67        29.79 
TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A8-A06O 
       25.15        20.61        10.29        14.93        17.92        13.02 
TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A086 TCGA-A8-A08G 
        1.02        18.97        10.98         9.99        13.02        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       37.05        31.00        30.97        12.00         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM 
       33.07         8.98        14.01        73.91         5.72        26.04 
TCGA-AC-A2QH TCGA-AC-A3QQ TCGA-AC-A5XU TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A041 
       33.04        24.13        14.96         8.22        20.19         0.23 
TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AO-A03L TCGA-AO-A03P 
        2.96         6.44         0.33         5.36        80.28        95.70 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KQ 
       26.04        20.32       115.27        98.27        70.42        61.87 
TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AW 
       32.52        98.33        83.87       103.86        61.28        86.53 
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       112.77       105.30 
TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0WV TCGA-B6-A0X1 
       98.66        93.30        71.05        54.21        79.46       245.10 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU 
       43.59        73.51        37.87        85.35        74.99        62.93 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 
       20.45        63.09        39.16        77.75        74.14        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0HQ TCGA-BH-A0HW 
       89.06        90.97        77.98        67.10        36.85        51.32 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EX 
       26.66        37.74        66.05        51.39        55.69        49.58 
TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A202 TCGA-BH-A203 
       25.81       114.15       122.83        63.35        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A5IZ TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 
       83.31        18.64        12.66        12.66        12.16        12.59 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A27A 
       11.34        11.28        12.33        12.95        15.45        24.56 
TCGA-C8-A3M8 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG 
       12.95        13.97        14.17        55.50        12.03        53.00 
TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       20.09        13.32        16.73        18.15        15.22        19.92 
TCGA-D8-A1XM TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y2 TCGA-D8-A27R TCGA-D8-A27W 
       17.69        16.31        16.54        14.24        10.09        12.26 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14R 
       43.00        34.42        46.59        40.11        44.68        38.60 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A15A TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B5 
       75.98        32.02        23.34        51.39        87.22        32.35 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1LA TCGA-E2-A1LK 
       77.65        70.36        33.73        28.44        24.59         8.75 
TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R2 
        8.28        38.76        34.16        35.24        24.82        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RH 
        6.12         3.02        11.15        48.23        46.65        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A2JS 
       47.64        34.45        38.37        41.72        38.99        29.72 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J2 TCGA-EW-A1OY TCGA-EW-A1P5 
       23.84        25.81        26.40        13.25        29.85        23.11 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6SA TCGA-GM-A2DC 
        6.15        13.94        52.73        17.52        16.77        83.34 
TCGA-GM-A2DK TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A5YM TCGA-LL-A73Y TCGA-LL-A7SZ 
       86.96        69.30         2.60        15.32        15.68        19.53 
TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A6VO TCGA-S3-A6ZG 
       12.36        22.39        22.32        41.92        28.21        18.48 
TCGA-S3-A6ZH TCGA-S3-AA10 
       21.07        19.27 

$`17Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I 
       19.56       107.70        23.61        31.36        24.26        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        11.05        53.06        19.99        15.06 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01        17.95         1.02        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT 
       19.79        14.53        19.33        13.71        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR 
        5.65         2.56        19.20        98.33        17.23        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       73.64        50.07        26.99        75.02        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       24.95        29.23        25.05        14.79        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU 
       18.87        13.94        11.41        52.96       108.07       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
      131.67        48.46        47.61         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       48.10        14.27        20.88        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       28.01        18.21       143.15        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV 
      114.81        92.48       107.93        77.19        75.25        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        67.33        34.55        61.58       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       80.28       118.45        79.76        74.40        72.00        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-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52         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-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-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 
       31.73        23.47        17.36        22.45        19.20        16.47 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       42.44        17.19        10.59        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW 
       91.07        32.75        56.28        35.93        50.83         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-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       35.31        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ 
       31.73        20.19        29.56        23.74        11.34        10.59 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       13.41        14.70        13.74        14.50        21.17        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 
       13.02         1.02        17.98        31.00        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        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-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I 
       18.05        36.95         0.99        38.01        28.96        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-A095 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       41.98         9.99        50.04         1.02        25.02        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-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04        19.23        22.95 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       60.92        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        14.83        22.19        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V 
       15.48        23.24        24.79        29.26        16.80        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       17.42        18.67        13.58        12.26         1.68         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        1.12         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         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         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         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.36         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-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        81.63        68.75        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 
       44.42        32.78        21.40        52.18        37.48        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       65.10        26.24        62.04        55.33        71.80       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
      108.72       106.78       108.03       102.31        82.68        60.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS 
       53.88        40.57        20.45        97.08        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TR 
       24.79        26.93       130.09        15.62       140.55         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        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       133.22       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      108.36       101.00        97.68        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M 
       99.32        37.81        94.29        86.43        33.73       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59       104.28        97.84       105.27       102.84 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       50.96        98.76        89.00        99.62        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.28       100.70        89.46       282.90       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        18.35        21.01       113.79       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.55       101.52       139.17       170.17 
TCGA-B6-A400 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
        7.07        68.12        18.84       103.63        71.15        59.84 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       25.55        81.44        39.55        70.22        84.13        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        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DH 
       85.87        49.94        77.95        46.39        81.73        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        81.83        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
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-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        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-A18M 
       32.91         4.90        35.93        20.12        90.84        72.56 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN 
       30.28        55.63        37.55         7.36        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY 
       91.99       113.82        82.85        42.28        12.00        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        97.48        25.08       120.62        33.17        74.73 
TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       33.99        55.00        45.63        72.07        53.98        55.50 
TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        57.83       130.16        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       110.60        20.88        23.51         9.63         5.26 
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-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.56        13.51        12.59        12.92        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HO TCGA-C8-A26V 
       12.33        10.92         0.16        12.03        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36        12.95        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.76        14.43        33.99        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        56.81        20.88        13.25        20.58        13.48 
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-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       18.90        14.01        18.97        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-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       21.83        14.50        55.30        16.41        15.85        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        43.04        15.32        15.52         9.93 
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 
       48.03        16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       25.22        27.52        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V 
       47.15        40.96        38.24        33.17        43.33        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IF 
       76.57        53.62        33.01        28.50        37.25        37.41 
TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       54.18        60.36        19.66        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      102.61        43.04        34.55        43.56        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       36.20        36.56        39.55        41.62        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A1RB 
       18.94         9.86        28.27         2.56        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A227 TCGA-E9-A228 
       40.24         1.12         6.58        21.27        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        41.03        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
        0.69         1.94         7.13        24.56        12.33         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       38.07        32.91        30.18        30.44        23.90        26.70 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.79        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.90        16.57        28.77        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90        19.99        10.52        14.43        34.55 
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-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       23.51        15.22        24.99        31.30        33.21         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH 
      109.87        59.57       216.76        79.10        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       85.15       115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
       32.75        17.06        14.70        14.47        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       16.08         7.46        19.59        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        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-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-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-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        9.93        18.81        20.68        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.23               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             245.1              282.9 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            30.985             27.120 
[1] "0.2 - 245.1 (31.0)" "0.0 - 282.9 (27.1)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED        16       16        1        2        80        48
  17Q GAIN WILD-TYPE      73       67        5        4       272       205
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1         31          8         12        4
  17Q GAIN WILD-TYPE         1        124         19         53       16
                    vv
clus                 STAGE X
  17Q GAIN MUTATED         1
  17Q GAIN WILD-TYPE      12
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  16                 73
  STAGE IA                 16                 67
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                80                272
  STAGE IIB                48                205
  STAGE III                 1                  1
  STAGE IIIA               31                124
  STAGE IIIB                8                 19
  STAGE IIIC               12                 53
  STAGE IV                  4                 16
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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    52 134  24  11
  17Q GAIN WILD-TYPE 222 491 113  29
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               52                222
  T2              134                491
  T3               24                113
  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   104  73  25  13
  17Q GAIN WILD-TYPE 402 285  94  64
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0              104                402
  N1               73                285
  N2               25                 94
  N3               13                 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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   187   5
  17Q GAIN WILD-TYPE 702  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    187    5
  17Q GAIN WILD-TYPE  702   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              187                702
  1                5                 17
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   213   8
  17Q GAIN WILD-TYPE 854   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    213    8
  17Q GAIN WILD-TYPE  854    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              213                854
  MALE                  8                  4
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    79 121
  17Q GAIN WILD-TYPE 358 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     79  121
  17Q GAIN WILD-TYPE  358  426
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                79                358
  YES              121                426
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q GAIN MUTATED                            0                           175
  17Q GAIN WILD-TYPE                          1                           593
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q GAIN MUTATED                               25                   1
  17Q GAIN WILD-TYPE                            176                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q GAIN MUTATED                       1                                6
  17Q GAIN WILD-TYPE                     8                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  17Q GAIN MUTATED                    4              9
  17Q GAIN WILD-TYPE                 13             37
D31V9, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 175                593
  INFILTRATING LOBULAR CARCINOMA                 25                176
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 24
  MUCINOUS CARCINOMA                              4                 13
  OTHER, SPECIFY                                  9                 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"
D31V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  1    13
  17Q GAIN WILD-TYPE                                0    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          39   143
  17Q GAIN WILD-TYPE                       142   601
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          13                 47
  BLACK OR AFRICAN AMERICAN                      39                142
  WHITE                                         143                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"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5 182
  17Q GAIN WILD-TYPE  34 692
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5  182
  17Q GAIN WILD-TYPE   34  692
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              182                692
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED   152  23
  18P GAIN WILD-TYPE 765 125
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               175                890 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                125 
$`18P GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A7-A2KD TCGA-A8-A091 TCGA-A8-A09K TCGA-AO-A1KT 
       19.20        38.30        22.32        33.01        29.98        17.79 
TCGA-AQ-A54N TCGA-E2-A15O TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-S3-AA12 
        2.56        50.79        73.64        26.99        14.79        18.87 
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM 
      133.05        48.46        31.79        73.84        87.25        24.79 
TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ TCGA-A2-A0YM 
       33.76       101.72        79.76         8.38        18.61        31.73 
TCGA-A2-A1FV TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       23.47        33.93        47.31        30.61        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06Z 
       20.19        14.50        21.17        10.29         9.37         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I 
       17.03         9.01         8.98        13.02        28.96        12.00 
TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09R TCGA-A8-A09W 
       31.00       112.08        43.00        12.00         8.98         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A62Y TCGA-AC-A6IW 
       27.02        17.03        73.05        33.04        17.42        13.58 
TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FY 
        1.68         0.33         1.78         0.33         7.96         0.33 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A TCGA-AO-A12F 
       95.70        32.78        55.33       115.27       102.31        60.56 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AQ 
       61.87        11.51        84.10        65.36       101.00        99.32 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LH 
       50.89       104.28       102.84        98.66        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       127.33       140.88 
TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A400 
      255.68       162.05       282.90        97.48        43.59         7.07 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD 
       85.35        68.12        61.51        74.89        46.39        81.73 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.65         2.56        79.00         4.41        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18T TCGA-BH-A1FC TCGA-BH-A1FU 
       31.00        23.05        37.74         7.36       114.15        55.50 
TCGA-BH-A208 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U 
       57.83         9.63         5.26        11.93        11.77        12.66 
TCGA-C8-A1HG TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JL 
       11.34        24.56        20.88        15.78        12.03        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1XW TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27N 
       21.01        13.32        43.04        14.24        13.05        17.06 
TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A15C 
       37.51        40.96        75.98        31.96        63.62        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1LH 
       17.29        18.21        22.19        11.08        60.36       106.75 
TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 
        8.28        22.29        34.16        35.24         9.86         2.56 
TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 
        6.12        45.01         1.12        46.59        40.73         0.69 
TCGA-E9-A249 TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 
        7.13        26.40        27.85        28.77        22.82        29.82 
TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-GI-A2C9 
       23.11        19.99        17.49        16.77        24.99       109.87 
TCGA-GM-A2DC TCGA-HN-A2NL TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ 
       83.34         2.60        14.47        16.08        15.68        19.53 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ 
       19.59        58.52        23.47        28.21         8.91         9.93 
TCGA-S3-A6ZG 
       18.48 

$`18P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E 
       11.28        11.97        11.05        53.06        29.03        19.99 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       15.06        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       45.07        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       50.24         5.65        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       21.44        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A1BC TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       16.47        50.07        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU 
       13.22        24.95        29.23        25.05        14.50        40.08 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALK 
       13.94        11.41        52.96       108.07       131.67        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
      101.98        55.43       136.73        99.12       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EN 
       56.81        67.33        34.55        61.58        25.22       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       118.45        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-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-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-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        23.77        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       20.25        19.20        16.47        52.47        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        36.23        39.65        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        56.28        35.93        50.37        50.83 
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-A0D9 TCGA-A7-A0DB 
       21.90        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       29.79        25.15        29.56        23.74        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        10.29        13.41        14.70        14.93        13.74 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX TCGA-A7-A6VY 
       17.92        14.73        12.10        10.72        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98        43.00        18.97        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-A08A TCGA-A8-A08B TCGA-A8-A08G 
       45.07        18.05        36.95         0.99        38.01        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08Z TCGA-A8-A092 
       37.05         9.99        31.00         0.99        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       41.98         9.99         9.99        12.00        50.04        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 
        1.02        25.02        19.04        15.02        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04         0.99        38.04        19.23 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
       22.95        73.91         5.72        22.26        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV 
       24.79        29.26        16.80        14.96        11.44        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         7.46         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 
        6.90         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 
        5.36         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        69.83        58.95        44.42 
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-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       65.10        26.24        62.04        71.80       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      106.78       108.03        98.27        82.68        70.42        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       40.57        20.45        97.08        82.62        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
      130.09        15.62        32.52       140.55        98.33         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        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 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      103.86        97.68        96.00        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22       120.33        99.78       118.59         2.76       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       97.84       105.27       105.30        50.96        98.76        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       93.30        85.64        71.05        93.83       166.42        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       38.96        10.59       281.29        11.90       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
       65.52       146.50       233.62        18.77        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      129.07        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       102.77       140.28       100.70        89.46       169.51 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.46        18.35        21.01       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        58.55       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A402 TCGA-B6-A409 
       73.51       139.17       170.17        37.87        74.99        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       63.09        81.44        39.55        39.16        70.22        84.13 
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        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       77.75        49.94        77.95        74.14        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
       78.28         3.22        67.86        70.88        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       14.30         9.63        44.81        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P 
       35.93        20.12        90.84        26.66        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       55.63        37.55        66.05        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-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.83        33.99        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        53.98        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FZ 
       10.52       110.60        20.88        18.64        23.51        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51        12.59        12.59        12.92        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.33        10.92        11.28         0.16        12.03        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       15.45        16.87        16.70         0.03         9.76        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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 
       56.81        13.25        20.58        13.97        14.17        13.48 
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        55.50        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       19.40        20.38        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        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        16.04        13.45        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         1.61        10.09        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        44.68        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y 
       38.60        33.17        43.33        34.26        32.02        69.34 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        69.96        23.24        19.43        21.04        23.87 
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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       33.73        33.70        28.44        59.18         3.88        60.99 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI 
       54.18        19.66        24.59        75.81        28.90       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
        8.75        43.04        34.55        43.56        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       36.20        36.56        39.55        41.62        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 
       18.94        24.82        28.27        34.95         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        32.09        40.24        46.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       38.37        41.03        41.72        40.50        20.12        38.99 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.79        25.81        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        16.57        25.94        29.95        29.85 
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-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-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       17.52        23.51        15.22        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       59.57       216.76        79.10        70.85        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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       10.62        32.75        17.06        15.32        14.70        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        2.63         7.46        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
        2.10        36.30        31.99        58.62        34.92        36.36 
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-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-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
       18.81        21.07        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.33               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            282.90             281.29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             26.40              28.47 
[1] "0.3 - 282.9 (26.4)" "0.0 - 281.3 (28.5)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED        10       14        0        2        74        35
  18P GAIN WILD-TYPE      79       69        6        4       278       218
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           1         19          6          8        4
  18P GAIN WILD-TYPE         1        136         21         57       16
                    vv
clus                 STAGE X
  18P GAIN MUTATED         3
  18P GAIN WILD-TYPE      10
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 14                 69
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                74                278
  STAGE IIB                35                218
  STAGE III                 1                  1
  STAGE IIIA               19                136
  STAGE IIIB                6                 21
  STAGE IIIC                8                 57
  STAGE IV                  4                 16
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    36 112  21   6
  18P GAIN WILD-TYPE 238 513 116  34
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               36                238
  T2              112                513
  T3               21                116
  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   100  44  17  13
  18P GAIN WILD-TYPE 406 314 102  64
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0              100                406
  N1               44                314
  N2               17                102
  N3               13                 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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   149   4
  18P GAIN WILD-TYPE 740  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    149    4
  18P GAIN WILD-TYPE  740   18
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              149                740
  1                4                 18
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   174   3
  18P GAIN WILD-TYPE 893   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    174    3
  18P GAIN WILD-TYPE  893    9
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE              174                893
  MALE                  3                  9
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    67  96
  18P GAIN WILD-TYPE 370 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     67   96
  18P GAIN WILD-TYPE  370  451
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                67                370
  YES               96                451
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P GAIN MUTATED                            0                           145
  18P GAIN WILD-TYPE                          1                           623
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P GAIN MUTATED                               15                   2
  18P GAIN WILD-TYPE                            186                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P GAIN MUTATED                       2                                5
  18P GAIN WILD-TYPE                     7                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  18P GAIN MUTATED                    0              7
  18P GAIN WILD-TYPE                 17             39
D32V9, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 145                623
  INFILTRATING LOBULAR CARCINOMA                 15                186
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  7                 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"
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                          49   101
  18P GAIN WILD-TYPE                       132   643
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                      49                132
  WHITE                                         101                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"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3 141
  18P GAIN WILD-TYPE  36 733
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  141
  18P GAIN WILD-TYPE   36  733
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO              141                733
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED   129  23
  18Q GAIN WILD-TYPE 788 125
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               152                913 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                23                125 
$`18Q GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A7-A2KD TCGA-A8-A091 TCGA-A8-A09K TCGA-AQ-A54N 
       19.20        38.30        22.32        33.01        29.98         2.56 
TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK 
       73.64        26.99        14.79       133.05        48.46        31.79 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ 
       73.84        87.25        24.79        33.76       101.72        79.76 
TCGA-A2-A0T2 TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25E TCGA-A2-A3XS 
        8.38        18.61        31.73        23.47       105.34        33.93 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A7-A0CJ TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A6VW 
       47.31        35.93        30.61        20.19        14.50         9.37 
TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I 
        9.01        10.98         8.98        13.02        28.96        12.00 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09R TCGA-A8-A0A9 TCGA-A8-A0AB 
      112.08        43.00        12.00         8.98        27.02        17.03 
TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AR 
       14.96        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       115.27       102.31        60.56        61.87        11.51 
TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LH 
       65.36       101.00        50.89       104.28        98.66        20.25 
TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RO 
      143.38       129.57       112.37       127.33       140.88       162.05 
TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BL 
       97.48        43.59         7.07        85.35        68.12        74.89 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       41.75        46.39        81.73        15.65         2.56        79.00 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HB TCGA-BH-A0HY 
        4.41         9.63        81.83        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        12.95        24.56        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        75.98        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        60.36 
TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NI 
      106.75         8.28        22.29        34.16        35.24         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22G 
       34.95         2.56         6.12        45.01         1.12        40.73 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1J6 
        0.69         7.13        38.07        26.40        27.85        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A6SA 
       22.82        29.82        23.11        19.99        17.49        16.77 
TCGA-EW-A6SB TCGA-GM-A2DC TCGA-LD-A7W5 TCGA-LL-A7SZ TCGA-OL-A66I TCGA-OL-A97C 
       24.99        83.34         7.10        19.53        23.47         8.91 
TCGA-S3-A6ZG TCGA-S3-AA10 
       18.48        19.27 

$`18Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E 
       11.28        11.97        11.05        53.06        29.03        19.99 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       15.06        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       45.07        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM 
       50.24        17.79         5.65        32.91        19.20        98.33 
TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       17.23        66.15        57.27        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 
       32.58        21.44        89.16         9.70        10.42        21.14 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 
       14.79        50.79        16.47        50.07        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      108.07       131.67        47.61        11.44         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       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       18.02        78.41       121.94       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       99.12       114.81        92.48       107.93        77.19        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-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       61.58        25.22       134.40        80.28       118.45        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-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-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-A0YT 
       21.90        21.67        49.48        19.33        48.46        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 
       17.36        60.72        22.45        20.25        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        42.44        17.19        18.15        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       39.65        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         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-A13H 
       35.67        33.11        29.79        31.73        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        13.74        21.17        17.92        14.73 
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-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98        43.00        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-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08G 
       45.07        18.05        36.95         0.99        38.01        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08Z 
       37.05         9.99        31.00        31.00         0.99        40.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       30.97        41.98         9.99         9.99        12.00        50.04 
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-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB 
       16.80        11.44        17.42        18.67        12.26         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-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        7.36         7.46         0.16         6.44         5.65         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         5.36         0.33         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-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        81.63        68.75        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        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-A0JJ TCGA-AO-A0JM 
       72.00        76.77        65.10        26.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D 
      113.62       108.72       106.78       108.03        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       70.42        53.88        40.57        20.45        97.08        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       98.33         5.26        84.10       109.02        75.22        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       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       125.16       108.36       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 
      102.84       105.30        50.96        98.76        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       93.30        85.64        71.05        93.83       166.42        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59        77.62       281.29        11.90       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN 
       50.70        65.52       146.50       233.62        18.77        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      165.76       129.07       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       263.28       102.77       140.28       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       282.90       169.51       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.01       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.55       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       37.87        74.99        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        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        43.53        61.51        21.70        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       77.95        74.14        89.06        90.97        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DV 
       38.01        29.98        13.91        78.28         3.22        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE 
       70.88        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 
       63.32        30.35        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        23.08        41.00        52.96        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-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
        5.59        23.93        24.95        42.35        44.81        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P 
        4.90        35.93        20.12        90.84        72.56        30.28 
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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        97.48        25.08       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       122.83        33.99        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        53.98        55.50        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A8FZ 
       20.12        10.52       110.60        20.88        23.51        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51        12.59        12.59        12.92        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.33        10.92        11.28         0.16        12.03        12.33 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
       16.87        16.70         0.03         9.76        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
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-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        53.00        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        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        48.03        16.41        13.48        17.06         1.61 
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        12.66        25.22        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        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       69.96        23.24        19.43        21.04        23.87        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       23.34        20.71        21.63        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L6 
       33.70        28.44        59.18         3.88        60.99        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK 
       19.66        24.59        75.81        28.90       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       43.04        34.55        43.56        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 
       34.29        17.69        34.82        32.88        36.82        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH 
       36.56        39.55        41.62        35.77        25.84        18.94 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB 
       24.82        28.27         3.02        11.15        48.23        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       41.03        41.72        40.50        20.12        38.99         1.94 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        12.33        29.72         9.47        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
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-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC 
       39.78        18.48        30.08         7.86        18.90         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-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       52.73        25.91        22.09        34.03        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       15.22        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        79.10        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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-A7W6 TCGA-LD-A9QF 
       62.47        11.84        11.57        21.24        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       32.75        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
        2.63        16.08        15.68         7.46        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        34.92        36.36        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        20.38        26.70        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-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-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       18.81        21.07        20.68        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.33               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            162.05             282.90 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             23.98              29.03 
[1] "0.3 - 162.1 (24.0)" "0.0 - 282.9 (29.0)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         9       10        0        2        62        33
  18Q GAIN WILD-TYPE      80       73        6        4       290       220
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           1         18          4          9        4
  18Q GAIN WILD-TYPE         1        137         23         56       16
                    vv
clus                 STAGE X
  18Q GAIN MUTATED         2
  18Q GAIN WILD-TYPE      11
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                 10                 73
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                62                290
  STAGE IIB                33                220
  STAGE III                 1                  1
  STAGE IIIA               18                137
  STAGE IIIB                4                 23
  STAGE IIIC                9                 56
  STAGE IV                  4                 16
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    29 101  18   5
  18Q GAIN WILD-TYPE 245 524 119  35
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               29                245
  T2              101                524
  T3               18                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
  18Q GAIN MUTATED    82  43  14  13
  18Q GAIN WILD-TYPE 424 315 105  64
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               82                424
  N1               43                315
  N2               14                105
  N3               13                 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"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED   134   4
  18Q GAIN WILD-TYPE 755  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    134    4
  18Q GAIN WILD-TYPE  755   18
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0              134                755
  1                4                 18
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED   151   3
  18Q GAIN WILD-TYPE 916   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    151    3
  18Q GAIN WILD-TYPE  916    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE              151                916
  MALE                  3                  9
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    63  80
  18Q GAIN WILD-TYPE 374 467
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     63   80
  18Q GAIN WILD-TYPE  374  467
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                63                374
  YES               80                467
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q GAIN MUTATED                            0                           127
  18Q GAIN WILD-TYPE                          1                           641
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q GAIN MUTATED                               13                   1
  18Q GAIN WILD-TYPE                            188                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q GAIN MUTATED                       1                                5
  18Q GAIN WILD-TYPE                     8                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  18Q GAIN MUTATED                    0              6
  18Q GAIN WILD-TYPE                 17             40
D33V9, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 127                641
  INFILTRATING LOBULAR CARCINOMA                 13                188
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  6                 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"
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                          38    92
  18Q GAIN WILD-TYPE                       143   652
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                      38                143
  WHITE                                          92                652
[1] 4 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     3 121
  18Q GAIN WILD-TYPE  36 753
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3  121
  18Q GAIN WILD-TYPE   36  753
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO              121                753
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED   165  21
  19P GAIN WILD-TYPE 752 127
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               186                879 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                21                127 
$`19P GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A093 TCGA-A8-A09E TCGA-AC-A5EI TCGA-AQ-A54O TCGA-AR-A2LR 
       38.30        17.95        49.05        14.53        32.91        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-E2-A1LG TCGA-GM-A2DD TCGA-LL-A5YP 
       73.35        81.63        54.05        50.07        75.02        14.79 
TCGA-S3-AA12 TCGA-W8-A86G TCGA-4H-AAAK TCGA-A1-A0SF TCGA-A1-A0SK TCGA-A2-A04Q 
       18.87        11.41        11.44        48.10        31.79        78.41 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET 
       75.25        67.33        34.55        33.76        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T6 TCGA-A2-A0YJ TCGA-A2-A1G1 
       34.29        63.29        50.43        18.90        18.61        19.20 
TCGA-A2-A3XU TCGA-A2-A3Y0 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DB 
       29.98        50.83        21.14        35.31        30.61        33.11 
TCGA-A7-A0DC TCGA-A7-A3J0 TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06X TCGA-A8-A07R 
       29.79        10.29        21.17        12.10        31.00         8.98 
TCGA-A8-A08X TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E 
       43.00        12.00        33.07         0.99        27.02        22.95 
TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OP 
       73.91        74.14        14.83        17.42        13.58        20.19 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX 
        0.33         1.78         7.36         7.00         0.36         0.33 
TCGA-AN-A0XN TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 
        0.33         5.59        80.28        81.63        32.78        20.32 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       55.33       115.27       106.78       102.31        98.27        82.68 
TCGA-AO-A1KS TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       11.51        65.36        61.28        86.53        86.43        50.89 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ TCGA-B6-A0I2 
      105.30        50.96        71.05        93.83        40.54       143.38 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      112.37       233.62       282.90        21.01       113.79       206.86 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0BA 
       43.59        73.51        85.35        62.93        20.45        37.22 
TCGA-BH-A0BJ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0E9 
       21.70        41.75        46.39        90.97        81.73        81.83 
TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T 
       30.35        36.85        90.84        37.74        55.63         7.36 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A6R9 
       51.16        91.99        57.83       130.16        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        12.16        12.33         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        17.06 
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        69.34        18.51        63.62        23.24        11.05 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LE TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N8 
       33.70        22.19        28.90        34.29        17.69        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22E 
       36.20        36.56        11.15        45.01         1.12        41.72 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A5FK 
       20.12         0.69         1.94         7.13        12.33        26.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB 
        0.79        26.40        28.77        29.82         7.86        19.99 
TCGA-EW-A1PD TCGA-EW-A423 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-HN-A2NL TCGA-LD-A7W6 
       13.94        17.52        24.99       109.87         2.60        13.28 
TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW 
       14.70         2.63        15.68        19.59        17.49        36.36 
TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        8.91         9.93        18.48        21.07        20.68        19.27 

$`19P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       29.03        19.99        15.06        33.01        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS 
        1.02        45.07        29.98        16.57        19.79        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       13.71        50.24        17.79         5.65         2.56        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       98.33        17.23        66.15        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U 
       73.64        26.99        15.68        52.96        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA17 
       24.95        29.23        25.05        14.50        40.08        13.94 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       52.96       108.07       133.05       131.67        48.46        47.61 
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-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
      143.15        18.02       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19         5.19        98.99       107.93        56.81 
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       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       74.40        72.00        31.82        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-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC 
        8.38        49.84        20.52        17.46        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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       60.72        22.45        20.25        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        91.07        32.75        56.28        47.31        35.93 
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-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       20.19        25.15        29.56        23.74        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.59        13.41        14.70        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       17.92        14.73        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Y 
        8.75        13.02        13.02         1.02        17.98        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        17.03        53.98         9.01        43.00        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-A085 
        7.99        24.99         9.99        45.07        18.05        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-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       40.01        30.97        41.98        12.00         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04         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-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04        19.23         5.72        22.26        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       16.31        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        29.26        16.80        14.96        11.44 
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         7.46         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         6.90         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 
        5.36        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 
       69.83        58.95        44.42        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-A0JJ TCGA-AO-A0JM 
       72.00        76.77        65.10        26.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      113.62       108.72       108.03        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       40.57        20.45        97.08        61.87        82.62        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AY 
       86.07        93.90        99.32        37.81        94.29        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
      104.28       112.77        97.84       105.27       102.84        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE 
       98.66        89.00        99.62        93.30        85.64       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 
       33.30        38.96        10.59        77.62       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
      275.87       129.57        50.70        65.52       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      162.05       102.77       140.28       100.70        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        79.46        18.35       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.55       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        74.99        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       71.15        59.84        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        84.13        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        85.87        77.75        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       74.14        89.06        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
        9.63        44.81        24.49        31.00        63.32        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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-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-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R 
       35.93        20.12        26.66        72.56        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        69.93       113.82        82.85        42.28 
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-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        25.08       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 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        28.14        26.14        38.60        83.31 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
       23.51         9.63        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-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.56        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.28         0.16        12.03        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       13.97        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       18.90        53.00        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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31        16.64        15.16        43.04 
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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.41        13.48         1.61        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        12.66        25.22        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        69.96        19.43        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       75.81       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 
       43.56         8.28        30.61        34.92        38.76        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       32.88        36.82        22.29        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB 
       34.95         2.56         6.12         3.02        48.23        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS 
       41.03        40.73        40.50        38.99        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       23.84        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        13.25        16.57        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 
       29.95        29.85        40.41        41.13        39.78        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08        18.90         6.15        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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       34.03        17.49        23.51        15.22        16.77        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21         7.40        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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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-JL-A3YX 
       72.03        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
       21.24         7.10        10.62        32.75        17.06        15.32 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        22.26        16.08         7.46        19.53        12.36 
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-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       58.62        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-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        18.81        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       17.39        17.26        17.03         3.81        66.84        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.03               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            282.90             281.29 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            28.835             28.140 
[1] "0.0 - 282.9 (28.8)" "0.0 - 281.3 (28.1)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED        14       13        1        2        76        39
  19P GAIN WILD-TYPE      75       70        5        4       276       214
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         23          5         12        0
  19P GAIN WILD-TYPE         2        132         22         53       20
                    vv
clus                 STAGE X
  19P GAIN MUTATED         0
  19P GAIN WILD-TYPE      13
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  14                 75
  STAGE IA                 13                 70
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                76                276
  STAGE IIB                39                214
  STAGE III                 0                  2
  STAGE IIIA               23                132
  STAGE IIIB                5                 22
  STAGE IIIC               12                 53
  STAGE IV                  0                 20
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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    39 119  23   6
  19P GAIN WILD-TYPE 235 506 114  34
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               39                235
  T2              119                506
  T3               23                114
  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
  19P GAIN MUTATED   102  54  19  12
  19P GAIN WILD-TYPE 404 304 100  65
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0              102                404
  N1               54                304
  N2               19                100
  N3               12                 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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   162   0
  19P GAIN WILD-TYPE 727  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    162    0
  19P GAIN WILD-TYPE  727   22
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0              162                727
  1                0                 22
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   183   4
  19P GAIN WILD-TYPE 884   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    183    4
  19P GAIN WILD-TYPE  884    8
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE              183                884
  MALE                  4                  8
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    72 100
  19P GAIN WILD-TYPE 365 447
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     72  100
  19P GAIN WILD-TYPE  365  447
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                72                365
  YES              100                447
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P GAIN MUTATED                            1                           139
  19P GAIN WILD-TYPE                          0                           629
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P GAIN MUTATED                               25                   2
  19P GAIN WILD-TYPE                            176                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P GAIN MUTATED                       3                                5
  19P GAIN WILD-TYPE                     6                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  19P GAIN MUTATED                    2             10
  19P GAIN WILD-TYPE                 15             36
D34V9, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 139                629
  INFILTRATING LOBULAR CARCINOMA                 25                176
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                 10                 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"
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                          36   133
  19P GAIN WILD-TYPE                       145   611
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                      36                145
  WHITE                                         133                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"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6 155
  19P GAIN WILD-TYPE  33 719
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  155
  19P GAIN WILD-TYPE   33  719
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 33
  NOT HISPANIC OR LATINO              155                719
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED   191  26
  19Q GAIN WILD-TYPE 726 122
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               217                848 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                122 
$`19Q GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A26I TCGA-A8-A093 TCGA-A8-A09E TCGA-AC-A5EI TCGA-AQ-A54N 
       38.30        21.73        17.95        49.05        14.53         2.56 
TCGA-AQ-A54O TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-E2-A1LG 
       32.91        57.27        73.35        81.63        54.05        50.07 
TCGA-GM-A2DD TCGA-LL-A5YP TCGA-S3-AA12 TCGA-W8-A86G TCGA-4H-AAAK TCGA-A1-A0SF 
       75.02        14.79        18.87        11.41        11.44        48.10 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A0CT TCGA-A2-A0D0 
       13.68        31.79        18.02        78.41        75.25        67.33 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EX 
       33.76        25.22        79.76        35.05        34.29        24.72 
TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T6 TCGA-A2-A0YH 
       63.29        50.43         8.38        49.84        18.90        21.67 
TCGA-A2-A1G0 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3Y0 TCGA-A2-A4S2 TCGA-A7-A0CJ 
       20.25        33.93        29.98        50.83        21.14        30.61 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE 
       33.11        29.79        31.73        10.29        14.50        21.17 
TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A08X TCGA-A8-A092 
       10.42        13.02        43.00         8.98        43.00        30.97 
TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09Q TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E 
       12.00        12.00        25.02         0.99        27.02        22.95 
TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OS 
       73.91        74.14        14.83        17.42        13.58         2.30 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW 
        0.33         1.78         7.36         0.16         7.00         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 
        0.33         0.33         5.59        81.63        32.78        20.32 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR 
      106.78       102.31        98.27        82.68        60.56        82.62 
TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW 
       11.51        98.33        98.93        65.36        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
       86.43        50.89       105.30        50.96        98.66        89.00 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ 
       71.05        93.83        40.54       143.38       112.37       233.62 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0WZ 
      165.76       140.88       100.70       282.90       113.79       206.86 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 
       43.59        73.51        85.35        62.93        20.45        39.55 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD 
       37.22        61.51        21.70        74.89        46.39        81.73 
TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N 
       81.83        30.35        36.85        90.84        26.66        37.74 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV 
       55.63         7.36        51.16        69.93        91.99        12.00 
TCGA-BH-A1EW TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A6R9 TCGA-C8-A12V TCGA-C8-A12W 
       55.69        57.83       130.16         5.26        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 
       12.16        12.03        12.33        12.95        15.45        16.70 
TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
        0.03        20.88        13.97        14.17        13.48        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JU 
       14.17        12.03        14.01        20.09        20.38        14.70 
TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27N TCGA-D8-A27R 
       17.79        21.83        12.99        43.04        17.06        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R 
       12.53        12.26        37.51        40.11        47.15        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A576 TCGA-E9-A1N8 
       21.63        11.05        33.70        22.19        34.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A22B 
       36.20        11.15        45.01         1.12        47.64        38.37 
TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-E9-A5FK 
       41.72         1.94         7.13        12.33        30.44        26.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PD 
        0.79        26.40        28.77        29.82         7.86        13.94 
TCGA-EW-A1PH TCGA-EW-A423 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-HN-A2NL TCGA-LD-A7W6 
       19.96        17.52        24.99        33.21         2.60        13.28 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5RW 
        2.63        15.68        19.59        17.49        22.39        36.36 
TCGA-OL-A66I TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
       23.47         8.91         9.93        18.48        21.07        20.68 
TCGA-S3-AA10 
       19.27 

$`19Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        33.01         1.02 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X 
       45.07        29.98        16.57        19.79        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       50.24        17.79         5.65        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       66.15        32.58        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A2P5 
       21.14        14.79        50.79        16.47        73.64        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       15.68        52.96        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA17 TCGA-WT-AB41 TCGA-Z7-A8R5 
       25.05        14.50        40.08        13.94        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SB 
      133.05       131.67        48.46        47.61         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM 
       14.37        43.43        14.27        47.24        20.88         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T 
       39.32        28.01        18.21       143.15       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
      114.81        92.48       107.93        77.19         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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       22.45        19.20        16.47        52.47        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        36.23        39.65        91.07 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW 
       32.75        56.28        47.31        35.93        50.37         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-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A13F 
       34.29        35.47        37.45        35.67        20.19        25.15 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF 
       29.56        23.74        20.61        11.34        10.59        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.70        14.93        13.74        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        10.29         9.37         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        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-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-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-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
        0.99       112.08        40.01        41.98         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        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        19.23         5.72        22.26        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       16.31        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        29.26        16.80        14.96        11.44 
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-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.32         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        2.96         1.71         9.96         7.46         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-A0FV TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        6.90         7.04         0.33         0.33         5.36         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-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.33        80.28        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 
       69.83        58.95        44.42        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E 
       71.80       115.27       113.62       108.72       108.03        70.42 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A04H 
       53.88        40.57        20.45        97.08        61.87        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR 
       26.93       130.09        15.62        32.52       140.55         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       84.10       109.02        75.22        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      101.00       103.86        97.68        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       99.32        37.81        94.29        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 
       97.84       105.27       102.84        98.76        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        39.39        33.30        38.96        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE 
      146.50        18.77       127.33        84.59       129.07       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       102.77       140.28        89.46       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        79.46        18.35        21.01       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.55       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        74.99        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
       71.15        59.84        25.55        63.09        81.44        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        51.68        32.02        18.21        43.53 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       77.75        49.94        77.95        74.14        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        24.49        31.00        63.32        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       20.12        72.56        30.28        37.55        66.05        51.39 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        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        53.98        55.50        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        18.64        23.51         9.63        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-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.59        12.59        12.92        12.46        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V 
       10.92        11.34        11.28         0.16        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A 
       12.53        12.36        12.95        16.87         9.76        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA 
       19.46        56.81        13.25        20.58        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       55.50        15.78        18.15        18.90        53.00        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        20.12        19.40        21.01        12.20        13.32 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.58        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        17.16        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        55.30        16.41        15.85        16.31        16.64 
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-A27P TCGA-D8-A27T TCGA-D8-A3Z5 
       48.03        16.41        13.48         1.61        13.08        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        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        46.59        40.41        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       34.26        32.02        19.43        21.04        23.87        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R 
       55.63        53.92         9.04        20.58        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.73        28.44        59.18         3.88        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 
        8.28        30.61        34.92        38.76        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        36.82        22.29        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       28.27        34.95         2.56         6.12         3.02        48.23 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09        40.24        46.65         6.58        21.27        46.59 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       34.45        32.05        42.25        37.74        39.09        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A 
       40.73        40.50        20.12         0.69        38.99        24.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       29.72         9.47        38.07        32.91        30.18        23.90 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       23.84        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        13.25        16.57        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 
       29.95        29.85        40.41        41.13        39.78        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99         6.15        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       34.03        17.49        23.51        15.22        16.77        31.30 
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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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-JL-A3YX 
       72.03        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
       21.24         7.10        10.62        32.75        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7SZ 
       14.70        14.47        22.26        16.08         7.46        19.53 
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-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       58.62        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-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-S3-A6ZF TCGA-S3-AA11 TCGA-S3-AA14 
       86.96         0.16         0.26        18.81        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.03               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            282.90             281.29 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             27.02              28.24 
[1] "0.0 - 282.9 (27.0)" "0.0 - 281.3 (28.2)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED        19       15        2        2        88        45
  19Q GAIN WILD-TYPE      70       68        4        4       264       208
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0         27          8         10        1
  19Q GAIN WILD-TYPE         2        128         19         55       19
                    vv
clus                 STAGE X
  19Q GAIN MUTATED         0
  19Q GAIN WILD-TYPE      13
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 15                 68
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA                88                264
  STAGE IIB                45                208
  STAGE III                 0                  2
  STAGE IIIA               27                128
  STAGE IIIB                8                 19
  STAGE IIIC               10                 55
  STAGE IV                  1                 19
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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    50 134  26   9
  19Q GAIN WILD-TYPE 224 491 111  31
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               50                224
  T2              134                491
  T3               26                111
  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   119  68  20  11
  19Q GAIN WILD-TYPE 387 290  99  66
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0              119                387
  N1               68                290
  N2               20                 99
  N3               11                 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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   196   1
  19Q GAIN WILD-TYPE 693  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    196    1
  19Q GAIN WILD-TYPE  693   21
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0              196                693
  1                1                 21
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   215   4
  19Q GAIN WILD-TYPE 852   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    215    4
  19Q GAIN WILD-TYPE  852    8
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE              215                852
  MALE                  4                  8
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    92 107
  19Q GAIN WILD-TYPE 345 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     92  107
  19Q GAIN WILD-TYPE  345  440
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                92                345
  YES              107                440
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q GAIN MUTATED                            0                           167
  19Q GAIN WILD-TYPE                          1                           601
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q GAIN MUTATED                               29                   3
  19Q GAIN WILD-TYPE                            172                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q GAIN MUTATED                       3                                6
  19Q GAIN WILD-TYPE                     6                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  19Q GAIN MUTATED                    2              9
  19Q GAIN WILD-TYPE                 15             37
D35V9, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 167                601
  INFILTRATING LOBULAR CARCINOMA                 29                172
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 24
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                  9                 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"
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    11
  19Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          39   156
  19Q GAIN WILD-TYPE                       142   588
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 49
  BLACK OR AFRICAN AMERICAN                      39                142
  WHITE                                         156                588
[1] 4 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     9 179
  19Q GAIN WILD-TYPE  30 695
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9  179
  19Q GAIN WILD-TYPE   30  695
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              179                695
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   347  59
  20P GAIN WILD-TYPE 570  89
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               406                659 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                59                 89 
$`20P GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A8-A06U TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09C 
       19.20        38.30        29.03        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AQ-A54O 
       49.05        45.07        29.98        19.33        50.24        32.91 
TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-D8-A146 TCGA-E2-A15O 
       19.20        66.15        73.35        81.63        21.14        50.79 
TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-S3-AA17 TCGA-W8-A86G TCGA-3C-AAAU TCGA-3C-AALI 
       15.68        75.02        13.94        11.41       133.05       131.67 
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       14.37        48.10        14.27        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS 
       39.32        18.02        55.43        99.12        24.79        77.19 
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-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY 
       25.22        79.76        35.05        34.29        31.82        63.29 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YD 
       27.12        44.88        50.43         8.38        20.75        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       21.90        21.67        18.61        23.77        17.36        60.72 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A4RX 
       20.25        19.20        36.23        33.93        91.07        24.39 
TCGA-A2-A4S2 TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        30.61        37.45        35.67        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-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O 
       14.93        14.50        14.73        10.29         9.37        13.02 
TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07P 
       17.98        26.01        17.03        53.98         9.01        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-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A092 TCGA-A8-A095 
       12.00        37.05        31.00         0.99        30.97        41.98 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 
        9.99        50.04         1.02         8.98        12.00         0.99 
TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH 
       27.02        73.91         5.72        99.35        26.04        33.04 
TCGA-AC-A2QJ TCGA-AC-A3QQ TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW 
       14.66        24.13        16.80        11.44        17.42        13.58 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04A 
        1.68        20.19         1.12         0.33         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FV TCGA-AN-A0FW 
        1.78         9.96         0.33         6.44         0.33         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M 
        0.33         5.36        12.33         0.30        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0J9 
       66.77        95.70        44.42        52.18        20.32        53.03 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       72.00        76.77        55.33        71.80       106.78       102.31 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       98.27        70.42        60.56        97.08        61.87        11.51 
TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 
       15.62        98.33       109.02        98.93        64.83        65.36 
TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H 
       83.87       108.36        93.90        61.28        86.53       160.90 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
      104.28       112.77        97.84       105.30        50.96        98.66 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-B6-A0I1 TCGA-B6-A0I2 
       89.00        85.64        93.83        54.21        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0RE 
      281.29       129.57        65.52       112.37       165.76       255.68 
TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC 
      212.25       162.05       282.90        79.46       113.79        43.59 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       73.51        85.35        74.99        68.12        18.84       103.63 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       62.93        20.45        37.22        43.53        61.51        74.89 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       75.48        77.75        49.94        74.14        41.75        46.39 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       81.73        67.10        78.28         4.41        14.30         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 
       81.83        31.00        63.32        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        25.08        33.99 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A5J0 TCGA-BH-A6R8 
       72.07        26.14        38.60        36.79        23.51         9.63 
TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        5.26        11.93        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        48.53        12.16        13.51        12.59 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 
       12.49        11.28        12.33        15.45        16.70         9.76 
TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       12.95        13.41        20.88        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        14.17        55.50        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        53.00        14.01        18.97        21.01        13.32 
TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XS TCGA-D8-A1XU 
       18.58        18.15        15.22        19.92        16.31        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27I 
       43.04        16.54        15.32        15.52         9.93        14.43 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27W TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A10B 
       16.41        13.48        12.26        16.18        25.22        37.51 
TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X 
       40.11        44.68        40.96        75.98        34.26        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 
       18.51        63.62        69.96        23.24        19.43        25.05 
TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
       22.82        12.92         9.04        76.57        53.62        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 
       33.73        33.70        22.19        60.99        60.36        19.66 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
      106.75       102.61         8.75         8.28        30.61        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
       34.29        17.69        22.29        34.16        36.20        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 
       35.77        35.24         9.86        24.82         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG 
        3.02        45.01        32.09        40.24         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       46.59        34.45        37.74        38.37        41.03        41.72 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       38.99         1.94         7.13        12.33        29.72        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 
       26.70         0.79        26.40         8.48        16.57        28.77 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC 
       29.85        41.13        23.11        18.48        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GM-A2DC 
       13.94        19.96        52.73        16.77        33.21        83.34 
TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A441 
       72.10        69.30         2.60        21.24         7.10        32.75 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ 
       15.32        14.70        22.26         2.63         7.46        19.53 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF 
       23.47        26.04         8.91        86.96         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-Z7-A8R6 
       18.48        19.27        17.03       107.05 

$`20P GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E 
       22.32        11.28        11.97        11.05        53.06        19.99 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       15.06        33.01        33.01        16.57        19.79        14.53 
TCGA-AC-A62X TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A1AM TCGA-AR-A1AR 
       13.71        17.79         5.65         2.56        98.33        17.23 
TCGA-AR-A2LR TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       57.27        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 
       10.42        14.79        16.47        73.64        50.07        26.99 
TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       52.96        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-WT-AB41 TCGA-Z7-A8R5 
       14.79        14.50        40.08        18.87        52.96       108.07 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE 
       48.46        47.61        11.44         9.96         8.52        43.43 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       47.24        31.79        28.01        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CK TCGA-A2-A0CO 
      121.94        73.84        87.25       101.98       136.73       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       92.48       107.93       107.93        34.55        61.58       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
      134.40        80.28       118.45        74.40        72.00        61.94 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       24.72        99.19        54.64        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YE 
       49.84        20.52        17.46        18.90        32.55        18.21 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       50.47        49.48        19.33        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       22.45        16.47        52.47        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
      105.34        10.59        39.65        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       47.31        35.93        50.37        50.83         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        26.96        21.90        35.31        34.29        35.47 
TCGA-A7-A13H TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SB 
       29.56        11.34        10.59        10.29        13.41        13.74 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX TCGA-A7-A6VY 
       21.17        17.92        12.10        10.72        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F 
       13.02         1.02        31.00         1.02        43.00        18.97 
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-A082 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L 
       18.05        36.95         0.99        28.96        19.96         9.99 
TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A099 
       31.00       112.08        43.00        40.01        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       12.00        33.07        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       14.01        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE 
       19.23        22.95        22.26        73.05        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB 
       90.71        60.92        87.12        74.14        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        14.83        22.19        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A6IV 
       15.48        23.24        24.79        29.26        14.96        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-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.62         1.71         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         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-A0XN 
        7.17         6.90         7.04         0.33         0.33         0.33 
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-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
       81.63        68.75        69.83        58.95        32.78        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       26.04        37.48        22.36        21.53        50.70        50.86 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       65.10        26.24        62.04       115.27       113.62       108.72 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
      108.03        82.68        53.88        40.57        20.45        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR 
       24.79        26.93       130.09        32.52       140.55         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 
       84.10        75.22        55.86       107.24       133.22       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       125.16       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY 
       86.07        99.32        37.81        94.29        86.43        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.27       102.84        98.76        99.62        93.30        71.05 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0IA 
       40.54        33.30        38.96        10.59        11.90       275.87 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70       146.50       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      129.07       140.88        68.45       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       102.77       140.28       100.70        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.01       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      245.10        28.27        68.94        58.55       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
      170.17        37.87         7.07        71.15        59.84        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       63.09        81.44        39.55        39.16        70.22        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       51.68        32.02        18.21        21.70        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 
       74.14        76.60        85.87        77.95        89.06        90.97 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ 
       77.98        38.01        29.98        13.91        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        79.00        67.86        70.88        16.27        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       44.81        24.49        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       24.56        52.96         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       51.32        23.93        24.95        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        26.66        72.56        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1FB 
       51.16       113.82        82.85        17.69        25.81       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       122.83        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 
       45.63        53.98        55.50        28.14        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
      130.16        36.82        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
       18.64        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
       12.66        12.56        12.59        12.92        12.46        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO 
       10.92        11.34         0.16        12.03        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 
       20.25        12.53        12.36        12.95        16.87         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ 
       24.56        14.43        33.99        13.02        12.49        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JJ 
       56.81        13.25        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-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58        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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.41        15.85        16.64        15.16        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N 
       17.42        16.04        13.45        13.05        48.03        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        10.09        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       21.67        12.66        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R 
       40.41        28.44        28.87        47.15        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 
       33.17        43.33        32.02        69.34        21.04        23.87 
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        55.63 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       53.92        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE 
       51.39        87.22        33.01        32.35        28.50        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU 
       37.41        70.36        28.44        59.18         3.88        11.08 
TCGA-E2-A1L6 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 
       54.18        24.59        75.81        28.90        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA 
       43.56        34.92        34.82        32.88        36.82        36.56 
TCGA-E9-A1NC TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R6 
       39.55        25.84        18.94        28.27        34.95        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
       48.23         1.12        46.65        47.64        32.05        42.25 
TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A24A 
       39.09        40.73        40.50        20.12         0.69        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       25.81        27.85        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 
       13.25        25.94        22.82        29.95        40.41        39.78 
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-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 
       17.52        23.51        15.22        24.99        31.30         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DI 
      109.87        59.57       216.76        79.10        70.85        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-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO 
       11.84        11.57        13.28        10.62        17.06        14.47 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       16.08        15.68        12.36        19.59        17.49        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-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-A66O TCGA-OL-A66P 
       26.70        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-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26        21.07        20.68        13.84        17.39        17.26 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        66.84        29.03        15.35        16.04 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.30               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            282.90             275.87 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             27.07              28.27 
[1] "0.3 - 282.9 (27.1)" "0.0 - 275.9 (28.3)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED        34       27        1        2       139        90
  20P GAIN WILD-TYPE      55       56        5        4       213       163
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           1         66         14         19       10
  20P GAIN WILD-TYPE         1         89         13         46       10
                    vv
clus                 STAGE X
  20P GAIN MUTATED         4
  20P GAIN WILD-TYPE       9
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  34                 55
  STAGE IA                 27                 56
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA               139                213
  STAGE IIB                90                163
  STAGE III                 1                  1
  STAGE IIIA               66                 89
  STAGE IIIB               14                 13
  STAGE IIIC               19                 46
  STAGE IV                 10                 10
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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    98 249  42  19
  20P GAIN WILD-TYPE 176 376  95  21
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               98                176
  T2              249                376
  T3               42                 95
  T4               19                 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"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED   191 125  61  24
  20P GAIN WILD-TYPE 315 233  58  53
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              191                315
  N1              125                233
  N2               61                 58
  N3               24                 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"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   355  10
  20P GAIN WILD-TYPE 534  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    355   10
  20P GAIN WILD-TYPE  534   12
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              355                534
  1               10                 12
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   401   9
  20P GAIN WILD-TYPE 666   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    401    9
  20P GAIN WILD-TYPE  666    3
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              401                666
  MALE                  9                  3
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   163 209
  20P GAIN WILD-TYPE 274 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    163  209
  20P GAIN WILD-TYPE  274  338
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               163                274
  YES              209                338
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P GAIN MUTATED                            0                           334
  20P GAIN WILD-TYPE                          1                           434
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P GAIN MUTATED                               45                   2
  20P GAIN WILD-TYPE                            156                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P GAIN MUTATED                       5                               10
  20P GAIN WILD-TYPE                     4                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  20P GAIN MUTATED                    1             12
  20P GAIN WILD-TYPE                 16             34
D36V9, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 334                434
  INFILTRATING LOBULAR CARCINOMA                 45                156
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                 12                 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"
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                          72   276
  20P GAIN WILD-TYPE                       109   468
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                      72                109
  WHITE                                         276                468
[1] 4 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    12 331
  20P GAIN WILD-TYPE  27 543
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12  331
  20P GAIN WILD-TYPE   27  543
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              331                543
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   384  63
  20Q GAIN WILD-TYPE 533  85
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               447                618 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                63                 85 
$`20Q GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 
       19.20        38.30        29.03        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A5EI 
        1.02        49.05        45.07        29.98        16.57        14.53 
TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A2LR 
       19.33        50.24        17.79        19.20        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A18H TCGA-D8-A146 TCGA-E2-A15O TCGA-EW-A1J5 
       73.35        81.63        21.44        21.14        50.79        15.68 
TCGA-GM-A2DD TCGA-S3-AA17 TCGA-W8-A86G TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA 
       75.02        13.94        11.41       133.05       131.67         9.96 
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       14.37        48.10        14.27        20.88        13.68         7.96 
TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS 
       18.02       101.98        55.43        99.12        24.79        77.19 
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-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY 
       25.22        79.76        35.05        34.29        31.82        63.29 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG 
       44.88        50.43        20.75        25.28        18.21        21.90 
TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 
       21.67        18.61        23.77        17.36        60.72        20.25 
TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT 
       19.20        42.44       105.34        36.23        33.93        91.07 
TCGA-A2-A3XX TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       47.31        24.39        21.14        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J 
       29.79        31.73        20.19        25.15        23.74        20.61 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        14.50        21.17        17.92        14.73 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       10.29        13.02        17.98        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-A08X TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09D 
        0.99        43.00        30.97        41.98         9.99        50.04 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 
       33.07         1.02         8.98        12.00         0.99        27.02 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ 
       73.91         5.72        99.35        26.04        33.04        14.66 
TCGA-AC-A3QQ TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO 
       24.13        16.80        11.44        17.42        13.58         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ 
       20.19         1.12         0.33         0.33         1.78         9.96 
TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.16         6.44         0.36         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
       12.33         0.30        80.28        61.35        66.77        81.63 
TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       69.83        44.42        52.18        20.32        53.03        72.00 
TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       76.77        55.33        71.80       106.78       102.31        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AQ-A04L 
       70.42        60.56        97.08        61.87        24.79       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       15.62        98.33       109.02        75.22        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       108.36       103.86        93.90        61.28 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       86.53       160.90        94.22       104.28       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A256 
      105.30        50.96        98.66        89.00        71.05        93.83 
TCGA-AR-A2LK TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB 
       54.21        77.62       143.38       281.29        11.90       129.57 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL 
       65.52       112.37       233.62       165.76       255.68        81.17 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF 
      162.05       282.90        79.46       113.79        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
       73.51       139.17        85.35        74.99        68.12        18.84 
TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0BA TCGA-BH-A0BF 
      103.63        62.93        20.45        25.55        37.22        43.53 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       75.48        77.75        49.94        74.14        41.75        46.39 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E2 
       81.73        67.10        78.28         3.22         4.41        14.30 
TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 
       81.83        31.00        63.32        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-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q 
       42.35        44.81        90.84        26.66        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        25.08        33.99 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28Q 
       45.63        72.07        26.14        38.60        57.83        36.79 
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-A12Y TCGA-C8-A130 
       12.66        12.66        12.66        12.66        48.53        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
       13.51        12.59        12.49        11.34        11.28        12.33 
TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M8 
       12.95        15.45        16.70         9.76        24.56        12.95 
TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       13.41        20.88        13.25        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        14.17        55.50        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JP 
       12.03        53.00        14.01        18.97        20.12        21.01 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       13.32        18.58        27.58        18.15        15.22        19.92 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.41        16.31        12.99        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R 
       15.52         9.93        14.43        16.41        13.48        10.09 
TCGA-D8-A27W TCGA-D8-A73X TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P 
       12.26        25.22        37.51        40.11        44.68        40.96 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A150 
       38.60        33.17        75.98        34.26        31.96        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       69.96        23.24        19.43        25.05        23.34        22.82 
TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 
       12.92         9.04        11.05        56.94        76.57        53.62 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 
       37.25        33.73        33.70        22.19        60.99        60.36 
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        38.76        34.29        17.69        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 
       34.16        36.20        35.77         9.86        24.82        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        11.15        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 
       40.24        46.65         6.58        21.27        46.59        34.45 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 
       37.74        38.37        41.03        41.72         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK 
        1.94         7.13        12.33        29.72        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OY 
        0.79        26.40         8.48        16.57        28.77        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC 
       40.41        41.13        23.11        18.48        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GI-A2C8 
       13.94        52.73        17.52        16.77        33.21         7.40 
TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A66U 
       83.34        85.15        69.30         2.60        11.84        21.24 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.10        32.75        15.32        14.70        22.26         2.63 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A97C 
       15.68        19.53        12.36        23.47        26.04         8.91 
TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       47.01        86.96         0.16         9.93        18.81        18.48 
TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-Z7-A8R6 
       19.27        17.03       107.05 

$`20Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E 
       22.32        11.28        11.97        11.05        53.06        19.99 
TCGA-A8-A084 TCGA-A8-A091 TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       15.06        33.01        19.79        13.71         5.65         2.56 
TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A1AR TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       32.91        98.33        17.23        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG 
        9.70        10.42        14.79        16.47        73.64        50.07 
TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       26.99        52.96        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-WT-AB41 
       25.05        14.79        14.50        40.08        18.87        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SE 
      108.07        48.46        47.61        11.44         8.52        43.43 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        31.79        39.32        28.01        18.21       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CO 
       78.41       121.94        73.84        87.25       136.73       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       92.48       107.93       107.93        34.55        61.58       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
      134.40        80.28       118.45        74.40        72.00        61.94 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 
       24.72        99.19        54.64        27.12        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-A0YC TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       32.55        50.47        49.48        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D 
       23.47        22.45        16.47        52.47        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        56.28        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         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-A13H 
       21.90        35.31        34.29        35.47        35.67        29.56 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SB TCGA-A7-A5ZV 
       11.34        10.59        10.29        13.41        13.74        12.10 
TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       31.00         1.02        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A085 
       12.00        32.05         9.99         7.99        18.05        36.95 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z 
        0.99        28.96         9.99        31.00       112.08        40.01 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       12.00         9.99        12.00        25.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB 
        0.99        14.01        19.04        13.02        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       38.04        19.23        22.95        22.26        73.05        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
       86.66        90.71        60.92        87.12        74.14        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM 
       32.45         6.48        16.31        14.83        22.19        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU 
       14.99        15.48        23.24        24.79        29.26        14.96 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS 
       18.67        12.26         8.22         0.03         1.32         2.30 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK 
        0.23         0.33         0.62         2.96         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        7.46         0.33         0.33         0.33         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         6.90         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-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       21.40        26.04        37.48        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 
       50.86        65.10        26.24        62.04       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      108.72       108.03        82.68        53.88        40.57        20.45 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR 
       82.62        11.51        26.93        32.52       140.55         5.26 
TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       84.10        55.86        65.36       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      125.16       101.00        97.68        96.00        86.07        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M 
       37.81        94.29        86.43        33.73        50.89       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
       99.78       118.59         2.76       105.27       102.84        98.76 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       99.62        93.30        85.64       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
       10.59       275.87        50.70       146.50        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       129.07       140.88        68.45       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       263.28       102.77       140.28       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
      169.51        97.48       188.68        18.35        21.01       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A2IU 
      129.70       245.10        28.27        68.94        58.55       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 
       37.87         7.07        71.15        59.84        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        70.22        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 
       74.14        76.60        85.87        77.95        89.06        90.97 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DS 
       77.98        38.01        29.98        13.91        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       79.00        67.86        70.88        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       44.81        24.49        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       24.56        52.96         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       51.32        23.93        24.95        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       35.93        20.12        72.56        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1FB 
       51.16       113.82        82.85        17.69        25.81       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       122.83        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       53.98        55.50        28.14        83.31       130.16        36.82 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A8FZ 
       20.12        10.52       110.60        20.88        18.64        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        12.56 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ 
       12.59        12.92        12.46        12.33        10.92         0.16 
TCGA-C8-A1HK TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.03        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ 
       16.87         0.03        14.43        33.99        13.02        12.49 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JJ 
       19.46        56.81        20.58        17.49        16.50        20.09 
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-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-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT 
       21.83        14.50        17.69        55.30        15.85        16.64 
TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.16        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       13.05        48.03        17.06         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 
       33.37        18.51        21.67        16.18        12.66        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        46.59        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z 
       47.15        38.24        43.33        32.02        69.34        18.51 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       21.04        23.87        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T 
       55.63        53.92        20.58        19.56        14.07        51.39 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF 
       87.22        33.01        32.35        28.50        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 
       70.36        28.44        59.18         3.88        11.08        54.18 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       24.59        75.81        28.90        43.04        34.55        43.56 
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        41.62        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RI 
       25.84        18.94        28.27        48.23         1.12        47.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       32.05        42.25        39.09        40.73        40.50        20.12 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       23.90        25.81        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 
       18.90        13.25        25.94        22.82        29.95        39.78 
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-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C9 
       17.49        23.51        15.22        24.99        31.30       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       59.57       216.76        79.10        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        62.47        11.57 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z 
       13.28        10.62        17.06        14.47        16.08         7.46 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        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-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        17.36        14.07        28.21        19.73        40.11 
TCGA-PE-A5DD TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 
       64.21         0.26        21.07        20.68        13.84        17.39 
TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.26         3.81        66.84        29.03        15.35        16.04 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.16               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            282.90             275.87 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            27.020             28.355 
[1] "0.2 - 282.9 (27.0)" "0.0 - 275.9 (28.4)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED        34       30        2        2       153       101
  20Q GAIN WILD-TYPE      55       53        4        4       199       152
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           1         71         15         25        9
  20Q GAIN WILD-TYPE         1         84         12         40       11
                    vv
clus                 STAGE X
  20Q GAIN MUTATED         4
  20Q GAIN WILD-TYPE       9
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  34                 55
  STAGE IA                 30                 53
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA               153                199
  STAGE IIB               101                152
  STAGE III                 1                  1
  STAGE IIIA               71                 84
  STAGE IIIB               15                 12
  STAGE IIIC               25                 40
  STAGE IV                  9                 11
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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   101 281  44  22
  20Q GAIN WILD-TYPE 173 344  93  18
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              101                173
  T2              281                344
  T3               44                 93
  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   208 139  64  29
  20Q GAIN WILD-TYPE 298 219  55  48
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              208                298
  N1              139                219
  N2               64                 55
  N3               29                 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"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   387  10
  20Q GAIN WILD-TYPE 502  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    387   10
  20Q GAIN WILD-TYPE  502   12
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              387                502
  1               10                 12
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   442   8
  20Q GAIN WILD-TYPE 625   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    442    8
  20Q GAIN WILD-TYPE  625    4
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              442                625
  MALE                  8                  4
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   180 231
  20Q GAIN WILD-TYPE 257 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    180  231
  20Q GAIN WILD-TYPE  257  316
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               180                257
  YES              231                316
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q GAIN MUTATED                            0                           368
  20Q GAIN WILD-TYPE                          1                           400
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q GAIN MUTATED                               49                   1
  20Q GAIN WILD-TYPE                            152                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q GAIN MUTATED                       6                               10
  20Q GAIN WILD-TYPE                     3                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  20Q GAIN MUTATED                    1             15
  20Q GAIN WILD-TYPE                 16             31
D37V9, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 368                400
  INFILTRATING LOBULAR CARCINOMA                 49                152
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                 15                 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"
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                          81   298
  20Q GAIN WILD-TYPE                       100   446
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                      81                100
  WHITE                                         298                446
[1] 4 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    12 366
  20Q GAIN WILD-TYPE  27 508
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12  366
  20Q GAIN WILD-TYPE   27  508
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              366                508
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   160  37
  21Q GAIN WILD-TYPE 757 111
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               197                868 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                37                111 
$`21Q GAIN MUTATED`
TCGA-A7-A26H TCGA-A7-A26I TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09K TCGA-AO-A1KT 
       23.80        21.73        33.01        17.95        29.98        17.79 
TCGA-AQ-A54O TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-E2-A15O TCGA-E2-A1LG 
       32.91        17.23        57.27        73.35        50.79        50.07 
TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-W8-A86G TCGA-3C-AAAU TCGA-A1-A0SI TCGA-A1-A0SJ 
       26.99        14.79        11.41       133.05        20.88        13.68 
TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CU TCGA-A2-A0EQ 
       28.01        18.02        87.25        24.79         5.19        79.76 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       63.29        99.19        27.12        17.13         8.38        49.84 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3KD TCGA-A2-A3XU 
       18.21        21.90        31.73        19.20        39.65        29.98 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       56.28        47.31        26.96        35.67        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O 
       20.19        25.15        13.74        21.17        10.29        13.02 
TCGA-A8-A06Q TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07R TCGA-A8-A07U 
        1.02        26.01        17.03        53.98         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X 
        9.99        45.07        38.01         9.99        31.00        43.00 
TCGA-A8-A092 TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2FM 
       30.97         1.02        14.01        17.03        73.91        26.04 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A0AS 
       33.04        14.66        17.42        13.58         0.33         0.33 
TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JM TCGA-AO-A128 
        7.04         0.33        66.77        81.63        71.80       106.78 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A1AJ 
       98.27        82.68        98.93        55.86        65.36       101.00 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A251 
       61.28        86.43        50.89       112.77        98.66        99.62 
TCGA-B6-A0I1 TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ 
       77.62       112.37        18.77        84.59       165.76       140.88 
TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI 
      255.68       162.05       282.90       113.79       101.52        73.51 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AY TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BR 
       74.99        18.84        25.55        84.13        74.89        76.60 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EB 
       77.75        74.14        46.39         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        55.50        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        12.56        12.16        13.51        12.59        12.92 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-D8-A13Y TCGA-D8-A13Z 
       12.33        12.95         0.03         9.76        56.81        20.88 
TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1XD TCGA-D8-A1XJ 
       19.20        53.00        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        43.04        37.51        44.68        40.96 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 
       38.60        31.96        18.51        69.96        19.43        25.05 
TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1IN TCGA-E2-A1L9 TCGA-E2-A1LE 
       11.05        76.57        53.62        22.19        19.66        28.90 
TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE 
        8.75        34.92        17.69        48.23         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A5UP 
       46.59        41.03         0.69        29.72        30.44        26.40 
TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PH 
       40.41        29.82        23.11         7.86         6.15        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-LD-A7W5 
       55.00        25.91        17.52        83.34        70.85         7.10 
TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
       32.75        14.47        15.68         7.46        12.36        19.59 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UL-AAZ6 
       36.36        20.38        20.68        19.27        17.03 

$`21Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09E 
       19.99        15.06        33.01        33.01         1.02        49.05 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       45.07        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL 
       50.24         5.65         2.56        19.20        98.33        66.15 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-EW-A1J5 
       10.42        21.14        14.79        16.47        73.64        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 
       25.05        14.50        40.08        18.87        13.94        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
      108.07       131.67        48.46        47.61        11.44         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-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       31.79         7.96        39.32        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        73.84       101.98        55.43       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV 
      114.81        92.48       107.93        77.19        75.25        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-A0ER 
       25.22       101.72       134.40        80.28       118.45        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-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 
       54.64        44.88        50.43        44.28        17.52        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-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT 
       21.67        49.48        18.61        19.33        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       23.47        17.36        60.72        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY TCGA-A2-A3XZ 
       36.23        33.93        91.07        32.75        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        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-A0DB TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       33.11        29.56        23.74        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF 
       10.29        13.41        14.70        14.93        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.72         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       13.02        17.98        31.00         1.02         9.01        43.00 
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-A085 TCGA-A8-A086 TCGA-A8-A08A 
       10.98         7.99        18.05        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08R 
       28.96        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
      112.08        40.01        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       12.00        50.04        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        19.23        22.95         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH 
       60.92        87.12        74.14        19.33        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       11.44        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-A041 
       20.19         1.12         1.32         2.30         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-A0AT TCGA-AN-A0FD 
        7.36         7.46         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         6.90 
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         5.36         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 
       69.83        58.95        44.42        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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       62.04        55.33       115.27       113.62       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      102.31        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       97.08        61.87        82.62        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
      130.09        15.62        32.52       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U1 
       84.10       109.02        75.22        64.83       107.24       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK 
       83.87       134.14       107.21       125.16       108.36       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       94.29        86.53        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       104.28        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 
      102.84       105.30        50.96        98.76        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IM 
      129.57        50.70        65.52       146.50       233.62       127.33 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      129.07        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       102.77       140.28       100.70        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
       97.48       188.68        79.46        18.35        21.01       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 
      139.17       170.17        37.87         7.07        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        62.93        59.84        20.45        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA 
       81.44        39.55        39.16        70.22        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        43.53        61.51        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       72.23        75.48        74.14        85.87        49.94        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        89.06        90.97        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       14.30        44.81        81.83        63.32        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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        32.91         4.90        35.93 
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-A1EO 
       37.55        66.05         7.36        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        97.48        25.08       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       53.98        28.14        83.31        57.83       130.16        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
       36.79        20.12        10.52       110.60        20.88        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26        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-A12Y TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
       12.66        12.66        48.53        12.59        12.46        12.49 
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-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       12.95        12.33        20.25        12.53        12.36        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
       16.87        16.70        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 
       13.02        12.49        13.41        19.46        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       55.50        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        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        48.03        16.41        13.48        17.06         1.61 
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        12.66        25.22        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        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       32.02        69.34        63.62        23.24        21.04        23.87 
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-A15P 
       12.92        55.63        53.92         9.04        20.58        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        14.07        51.39        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI 
       54.18        60.36        24.59        75.81       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       43.04        34.55        43.56         8.28        30.61        38.76 
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        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        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        11.15        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       40.24         6.58        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       12.33         9.47        38.07        32.91        30.18        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        26.70         0.79        25.81        27.85        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-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-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       39.78        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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       33.21         7.40       109.87        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-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        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       21.24        13.28        10.62        17.06        15.32        14.70 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       22.26         2.63        16.08        19.53        17.49        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-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-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-A6ZG 
       86.96         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ 
       21.07        13.84        17.39        17.26         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.03               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            282.90             281.29 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             28.01              28.24 
[1] "0.0 - 282.9 (28.0)" "0.0 - 281.3 (28.2)"
[1] "hr=" "1.5"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        13       12        1        1        72        39
  21Q GAIN WILD-TYPE      76       71        5        5       280       214
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0         32          3         16        4
  21Q GAIN WILD-TYPE         2        123         24         49       16
                    vv
clus                 STAGE X
  21Q GAIN MUTATED         3
  21Q GAIN WILD-TYPE      10
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  13                 76
  STAGE IA                 12                 71
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                72                280
  STAGE IIB                39                214
  STAGE III                 0                  2
  STAGE IIIA               32                123
  STAGE IIIB                3                 24
  STAGE IIIC               16                 49
  STAGE IV                  4                 16
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    47 122  22   5
  21Q GAIN WILD-TYPE 227 503 115  35
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               47                227
  T2              122                503
  T3               22                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
  21Q GAIN MUTATED    87  66  22  17
  21Q GAIN WILD-TYPE 419 292  97  60
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               87                419
  N1               66                292
  N2               22                 97
  N3               17                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   171   4
  21Q GAIN WILD-TYPE 718  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    171    4
  21Q GAIN WILD-TYPE  718   18
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0              171                718
  1                4                 18
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   196   2
  21Q GAIN WILD-TYPE 871  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    196    2
  21Q GAIN WILD-TYPE  871   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE              196                871
  MALE                  2                 10
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    71 112
  21Q GAIN WILD-TYPE 366 435
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     71  112
  21Q GAIN WILD-TYPE  366  435
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                71                366
  YES              112                435
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q GAIN MUTATED                            0                           169
  21Q GAIN WILD-TYPE                          1                           599
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q GAIN MUTATED                               17                   2
  21Q GAIN WILD-TYPE                            184                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q GAIN MUTATED                       4                                0
  21Q GAIN WILD-TYPE                     5                               30
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  21Q GAIN MUTATED                    1              5
  21Q GAIN WILD-TYPE                 16             41
D38V9, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 169                599
  INFILTRATING LOBULAR CARCINOMA                 17                184
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           4                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 30
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  5                 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"
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                          43   122
  21Q GAIN WILD-TYPE                       138   622
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                      43                138
  WHITE                                         122                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"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9 154
  21Q GAIN WILD-TYPE  30 720
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9  154
  21Q GAIN WILD-TYPE   30  720
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              154                720
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    82  15
  22Q GAIN WILD-TYPE 835 133
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                97                968 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                133 
$`22Q GAIN MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A8-A091 TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AQ-A0Y5 
       19.20        38.30        33.01        29.98        16.57         5.65 
TCGA-AR-A2LR TCGA-LL-A5YP TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A2-A04U TCGA-A2-A04W 
       57.27        14.79         9.96        31.79        87.25       101.98 
TCGA-A2-A0CL TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0T1 TCGA-A2-A1FV TCGA-A2-A1G1 
       99.12        56.81        33.76        17.13        23.47        19.20 
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-A09M TCGA-A8-A09X TCGA-AC-A23H TCGA-AC-A2QJ 
       38.01         0.99        33.07        14.01         5.72        14.66 
TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL 
       11.44         1.12         7.46         0.16         0.33         7.59 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A12G TCGA-AQ-A04L 
        0.33         0.33        98.27        60.56        53.88       130.09 
TCGA-AR-A0TP TCGA-AR-A0TV TCGA-AR-A0U1 TCGA-AR-A24U TCGA-AR-A24V TCGA-B6-A0RS 
      140.55        75.22       133.22       102.84       105.30       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A400 TCGA-B6-A402 TCGA-BH-A0BG 
      282.90        79.46        43.59         7.07        74.99        61.51 
TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0HY TCGA-BH-A18Q TCGA-BH-A18U 
       41.75        78.28        14.30        50.79        55.63        51.39 
TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       69.93        12.00        55.50        26.14        38.60        57.83 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A1HG 
       11.93        12.66        11.77        12.66        12.56        11.34 
TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JK TCGA-D8-A1XJ 
       13.97        15.78        18.15        18.90        20.12        21.83 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27W TCGA-E2-A14X TCGA-E2-A152 
       43.04        15.32        13.48        12.26        31.96        69.96 
TCGA-E2-A1B0 TCGA-E9-A1NC TCGA-E9-A22B TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A424 
       53.62        39.55        38.37        26.40        40.41        23.51 
TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A6FR TCGA-LL-A7SZ 
      109.87        70.85        69.30        15.32        16.08        19.53 
TCGA-LL-A8F5 
       19.59 

$`22Q GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       49.05        45.07        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM 
       50.24        17.79         2.56        32.91        19.20        98.33 
TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       17.23        66.15        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       21.44        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 
       50.79        16.47        73.64        50.07        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       25.05        14.50        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       52.96       108.07       133.05       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       11.44         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       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        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 
      118.45        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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 
       27.12        44.88        50.43        44.28        17.52         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-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW 
       18.61        19.33        48.46        31.73        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       60.72        22.45        20.25        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        91.07        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       35.93        50.37        50.83         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-A13D 
       35.47        30.61        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        29.56        23.74        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.29        13.41        14.70        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW 
       21.17        17.92        14.73        12.10        10.72         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G 
        1.02        17.03        53.98        43.00        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-A07Z TCGA-A8-A082 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        18.05        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       13.02         0.99        28.96        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00        31.00       112.08        43.00        40.01 
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-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04         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        19.23        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       16.80        14.96        17.42        18.67        13.58        12.26 
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-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-A0AR TCGA-AN-A0AT 
        1.78         1.71         9.96         7.36         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         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
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-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        69.83        58.95        44.42        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       65.10        26.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D 
      113.62       108.72       106.78       108.03       102.31        82.68 
TCGA-AO-A12E TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       70.42        40.57        20.45        97.08        61.87        82.62 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ 
       11.51        24.79        26.93        15.62        32.52        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        84.10       109.02        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       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.43        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      105.27        50.96        98.76        98.66        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       93.30        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       33.30        38.96        10.59        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       11.90       275.87       129.57        50.70        65.52       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       169.51        97.48       188.68        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        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        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.95        74.14        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP 
       77.98        67.10        38.01        29.98        13.91        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        79.00        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
        4.41        15.68         9.63        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        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        32.91         4.90        35.93        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        25.08       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 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       53.98        28.14        83.31       130.16        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        9.63         5.26        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.16        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.49        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95        15.45        16.87        16.70         0.03         9.76 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        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        56.81        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-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       55.50        12.03        53.00        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-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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.31        16.64        12.99        15.16        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        48.03        16.41        17.06         1.61 
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-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        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-A14Y TCGA-E2-A14Z 
       75.98        43.33        34.26        32.02        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       63.62        23.24        19.43        21.04        23.87        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        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        76.57        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE 
       22.29        34.16        36.20        36.56        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        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        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       45.01        32.09        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       37.74        39.09        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        41.13        39.78        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-A6S9 
       25.91        22.09        34.03        17.49        17.52        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        79.10        83.34        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
       32.75        17.06        14.70        14.47        22.26         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       15.68         7.46        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
       18.48        21.07        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.16               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            282.90             281.29 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             26.14              28.27 
[1] "0.2 - 282.9 (26.1)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         7        5        0        1        40        20
  22Q GAIN WILD-TYPE      82       78        6        5       312       233
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0         15          7          3        1
  22Q GAIN WILD-TYPE         2        140         20         62       19
                    vv
clus                 STAGE X
  22Q GAIN MUTATED         0
  22Q GAIN WILD-TYPE      13
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   7                 82
  STAGE IA                  5                 78
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                40                312
  STAGE IIB                20                233
  STAGE III                 0                  2
  STAGE IIIA               15                140
  STAGE IIIB                7                 20
  STAGE IIIC                3                 62
  STAGE IV                  1                 19
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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  65   9   7
  22Q GAIN WILD-TYPE 256 560 128  33
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               18                256
  T2               65                560
  T3                9                128
  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    52  28  11   4
  22Q GAIN WILD-TYPE 454 330 108  73
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               52                454
  N1               28                330
  N2               11                108
  N3                4                 73
[1] 4 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    86   1
  22Q GAIN WILD-TYPE 803  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     86    1
  22Q GAIN WILD-TYPE  803   21
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               86                803
  1                1                 21
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    98   1
  22Q GAIN WILD-TYPE 969  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     98    1
  22Q GAIN WILD-TYPE  969   11
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               98                969
  MALE                  1                 11
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    40  47
  22Q GAIN WILD-TYPE 397 500
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     40   47
  22Q GAIN WILD-TYPE  397  500
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                40                397
  YES               47                500
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q GAIN MUTATED                            0                            81
  22Q GAIN WILD-TYPE                          1                           687
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q GAIN MUTATED                                4                   1
  22Q GAIN WILD-TYPE                            197                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q GAIN MUTATED                       2                                2
  22Q GAIN WILD-TYPE                     7                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  22Q GAIN MUTATED                    1              8
  22Q GAIN WILD-TYPE                 16             38
D39V9, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  81                687
  INFILTRATING LOBULAR CARCINOMA                  4                197
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  8                 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"
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                          21    59
  22Q GAIN WILD-TYPE                       160   685
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                      21                160
  WHITE                                          59                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"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  84
  22Q GAIN WILD-TYPE  36 790
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   84
  22Q GAIN WILD-TYPE   36  790
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO               84                790
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED   128  21
  XP GAIN WILD-TYPE 789 127
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              149               916 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               127 
$`XP GAIN MUTATED`
TCGA-A7-A0CD TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-AC-A5EI TCGA-AC-A62X 
       38.30        33.01        33.01        17.95        14.53        13.71 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A18H TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO 
       57.27        73.35        21.44       131.67        13.68        28.01 
TCGA-A2-A0CL TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T1 
       99.12        56.81        33.76        79.76        44.88        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G0 
        8.38        49.84        21.90        18.61        31.73        20.25 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 TCGA-A7-A0DA 
       42.44       105.34        47.31        35.93        21.14        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A7-A5ZV TCGA-A8-A075 
       33.11        31.73        20.61        10.29        12.10        17.03 
TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       53.98        32.05        10.98         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08P 
       45.07        13.02        38.01        28.96        12.00        31.00 
TCGA-A8-A08T TCGA-A8-A095 TCGA-A8-A09Q TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A3OD 
      112.08        41.98        25.02         5.72        73.05        14.83 
TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AO-A03N 
        0.33         9.96         7.04         0.33         0.33        66.77 
TCGA-AO-A03O TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B 
       81.63        62.04        55.33        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        86.43       160.90 
TCGA-AR-A24Z TCGA-AR-A255 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 
       98.66        71.05       143.38       281.29       206.86       245.10 
TCGA-B6-A1KF TCGA-B6-A400 TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0BR TCGA-BH-A0BV 
      101.52         7.07        20.45        25.55        76.60        49.94 
TCGA-BH-A0DS TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18N TCGA-BH-A18Q 
        2.56        30.35        36.85        12.89        37.74        55.63 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A202 
       91.99        82.85        12.00        25.81       114.15        26.14 
TCGA-BH-A209 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A130 TCGA-C8-A1HO 
      130.16         9.63        11.93        11.77        12.16        12.33 
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        43.04 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14S 
       15.32        14.14        12.53        18.51        37.51        33.17 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15K TCGA-E2-A1B0 
       34.26        31.96        19.43        17.29         9.04        53.62 
TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NF 
        8.28        34.92        17.69        22.29        36.20        35.24 
TCGA-E9-A1RC TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PB 
       40.24        29.72        23.90         0.79         8.48        19.99 
TCGA-GI-A2C9 TCGA-GM-A3XL TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-OL-A5DA TCGA-OL-A97C 
      109.87        69.30         2.63        15.68        58.62         8.91 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-WT-AB44 TCGA-Z7-A8R6 
        9.93        18.81        20.68        29.03       107.05 

$`XP GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       21.73        22.32        11.28        11.97        11.05        53.06 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09E 
       29.03        19.99        15.06        33.01         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AO-A0JI 
       45.07        29.98        16.57        19.79        19.33        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM 
       17.79         5.65         2.56        32.91        19.20        98.33 
TCGA-AR-A1AR TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       17.23        66.15        81.63        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
      108.07       133.05        48.46        47.61        11.44         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-A0SQ TCGA-A2-A04N 
       20.88        31.79         7.96        39.32        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       18.02        78.41       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        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-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      118.45        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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       50.43        44.28        17.52        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-A1G6 TCGA-A2-A259 TCGA-A2-A25C 
       60.72        22.45        19.20        16.47        52.47        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        32.75        56.28        50.37        50.83         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-A13E 
       34.29        35.47        30.61        37.45        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF 
       25.15        29.56        23.74        11.34        10.59        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       14.70        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        1.02         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08A 
       12.00         9.99         7.99        18.05        36.95         0.99 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X 
       19.96        37.05         9.99        31.00         0.99        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        30.97        12.00         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        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-A23E 
        0.99        27.02        17.03        38.04        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       73.91        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ 
       14.66        32.45         6.48        16.31        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       16.80        14.96        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-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.78         1.71         7.36         7.46         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-A0FW 
        7.00         7.59         7.17         6.90         0.33         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       61.35        95.70        68.75        69.83        58.95        44.42 
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-A124 TCGA-AO-A125 TCGA-AO-A126 
       76.77        65.10        26.24       115.27       113.62       108.72 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03       102.31        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        20.45        97.08        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
       98.33        84.10       109.02        75.22        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       133.22       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       93.90        99.32        37.81        94.29        86.53        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        98.76        89.00        99.62        93.30        85.64 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.28       100.70        89.46       282.90       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.46        18.35        21.01       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        58.55        43.59        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
      170.17        37.87        85.35        74.99        68.12        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        62.93        59.84        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        84.13        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        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        72.23        75.48        74.14        85.87        77.75 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        74.14        41.75        46.39        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       78.28        15.65         3.22        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       81.83        24.49        31.00        63.32        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.39        53.26        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-A0HW 
       26.50        20.38         5.85         2.50        13.61        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        32.91         4.90        35.93        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-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       55.69        49.58        17.69        31.53        97.48        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.83        33.99        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        53.98        55.50        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31        57.83        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 
       10.52       110.60        20.88        18.64        23.51         5.26 
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-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        12.33        12.95        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A 
       12.95        15.45        16.87        16.70         9.76        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        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        56.81        20.88        13.25        20.58        13.48 
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        55.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JM 
       18.90        12.03        53.00        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        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY 
       15.85        16.31        16.64        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        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        1.61        10.09        13.08        12.26        33.37        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        43.00        34.42        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-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        38.60        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E 
       21.04        23.87        25.05        23.34        22.82        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L 
       21.63        18.21        12.92        55.63        53.92        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 
        8.75        43.04        34.55        43.56        30.61        38.76 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA 
       34.29        34.82        32.88        36.82        34.16        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       39.55        41.62        35.77        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        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 
       11.15        48.23        45.01        32.09         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        7.13        24.56        12.33         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        30.44        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       27.85        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90         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-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        70.85        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-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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.62        32.75        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       22.26        16.08         7.46        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       31.99        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-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG 
       47.01        64.21        86.96         0.16         0.26        18.48 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       21.07        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A 
        3.81        66.84        15.35        16.04 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.03              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           281.29            282.90 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            28.01             28.24 
[1] "0.0 - 281.3 (28.0)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED        12        8        2        2        55        32
  XP GAIN WILD-TYPE      77       75        4        4       297       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  XP GAIN MUTATED           0         23          3          9        4       0
  XP GAIN WILD-TYPE         2        132         24         56       16      13
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 8                75
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               55               297
  STAGE IIB               32               221
  STAGE III                0                 2
  STAGE IIIA              23               132
  STAGE IIIB               3                24
  STAGE IIIC               9                56
  STAGE IV                 4                16
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    29  98  19   4
  XP GAIN WILD-TYPE 245 527 118  36
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              29               245
  T2              98               527
  T3              19               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
  XP GAIN MUTATED    73  45  20  10
  XP GAIN WILD-TYPE 433 313  99  67
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              73               433
  N1              45               313
  N2              20                99
  N3              10                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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED   129   5
  XP GAIN WILD-TYPE 760  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    129    5
  XP GAIN WILD-TYPE  760   17
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0             129               760
  1               5                17
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED   149   1
  XP GAIN WILD-TYPE 918  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    149    1
  XP GAIN WILD-TYPE  918   11
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE             149               918
  MALE                 1                11
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    57  83
  XP GAIN WILD-TYPE 380 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     57   83
  XP GAIN WILD-TYPE  380  464
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               57               380
  YES              83               464
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP GAIN MUTATED                            1                           122
  XP GAIN WILD-TYPE                          0                           646
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP GAIN MUTATED                               11                   3
  XP GAIN WILD-TYPE                            190                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP GAIN MUTATED                       2                                4
  XP GAIN WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  XP GAIN MUTATED                    2              5
  XP GAIN WILD-TYPE                 15             41
D40V9, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                122               646
  INFILTRATING LOBULAR CARCINOMA                11               190
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 5                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"
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                          32    91
  XP GAIN WILD-TYPE                       149   653
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                     32               149
  WHITE                                         91               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"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3 119
  XP GAIN WILD-TYPE  36 755
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3  119
  XP GAIN WILD-TYPE   36  755
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             119               755
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   119  17
  XQ GAIN WILD-TYPE 798 131
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              136               929 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               17               131 
$`XQ GAIN MUTATED`
TCGA-A7-A0CD TCGA-A7-A2KD TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-AC-A5EI 
       38.30        22.32        33.01        33.01        17.95        14.53 
TCGA-AC-A62X TCGA-AR-A5QM TCGA-BH-A18H TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04T 
       13.71        73.35        21.44        13.68        28.01        73.84 
TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T2 
       24.79        56.81        33.76        79.76        44.88         8.38 
TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25E 
       49.84        21.90        18.61        31.73        20.25       105.34 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A26J 
       47.31        35.93        21.14        33.11        31.73        20.61 
TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A8-A076 TCGA-A8-A07L 
       10.29        14.70        14.50        12.10        53.98        32.05 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B 
       10.98         8.98         9.99        45.07        13.02        38.01 
TCGA-A8-A08C TCGA-A8-A08T TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09Q TCGA-A8-A09W 
       28.96       112.08        41.98        12.00        25.02         0.99 
TCGA-AC-A2BK TCGA-AC-A3OD TCGA-AN-A03Y TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY 
       73.05        14.83         0.33         7.04         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A0JM 
       66.77        81.63        32.78        52.18        55.33        71.80 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TW TCGA-AR-A1AV 
      106.78        98.27        60.56        82.62        98.93        61.28 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A254 TCGA-B6-A0I2 TCGA-B6-A0I5 
      104.28       112.77        98.66        85.64       143.38       281.29 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0DL 
      206.86       245.10       101.52        20.45        25.55        78.28 
TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A0HY 
        2.56         9.63        63.32        30.35        36.85        50.79 
TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1F0 
       23.05        37.74        55.63        91.99        82.85        25.81 
TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12M 
      114.15        26.14       130.16         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        16.70         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        43.04        15.32        12.53 
TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y 
       18.51        37.51        33.17        34.26        31.96        69.34 
TCGA-E2-A15D TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1RC 
       17.29        53.62         8.28        17.69        22.29        40.24 
TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1P5 TCGA-EW-A1PB 
       29.72        23.90         0.79         8.48        23.11        19.99 
TCGA-GI-A2C9 TCGA-GM-A3XL TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-OL-A66I TCGA-OL-A97C 
      109.87        69.30         2.63        15.68        23.47         8.91 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-Z7-A8R6 
        9.93        18.81        20.68       107.05 

$`XQ GAIN WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       21.73        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
       19.99        15.06        33.01         1.02        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT 
       29.98        16.57        19.79        19.33        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
        5.65         2.56        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       66.15        57.27        81.63        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SQ 
       47.24        20.88        31.79         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W 
      143.15        18.02        78.41       121.94        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        99.12       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        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-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      118.45        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-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-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-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        60.72        22.45        19.20        16.47        52.47 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       42.44        17.19        18.15        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       33.93        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         7.30        24.39        21.30        23.21        26.96 
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-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G 
       35.67        29.79        20.19        25.15        29.56        23.74 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       11.34        10.59        13.41        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       17.92        14.73        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        17.98        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
       26.01         1.02        17.03         9.01        43.00        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U 
       18.97        14.01        12.00         9.99         7.99        24.99 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       18.05        36.95         0.99        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00        31.00         0.99        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       30.97         9.99         9.99        12.00        50.04        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 
        1.02         8.98        19.04        15.02        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
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-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         7.46         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-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ 
        7.59         7.17         6.90         0.33         0.36         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         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-A0J3 
       95.70        68.75        69.83        58.95        44.42        21.40 
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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       62.04       115.27       113.62       108.72       108.03       102.31 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       82.68        70.42        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       61.87        11.51        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       75.22        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        94.29        86.53        86.43        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       120.33        99.78       118.59         2.76 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27       102.84       105.30        50.96        98.76 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        99.62        93.30        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 
       40.54        33.30        38.96        10.59        77.62        11.90 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.52       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      233.62        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.28       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       169.51        97.48       188.68        79.46 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       18.35        21.01       113.79       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.55        43.59        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        74.99        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       71.15        62.93        59.84        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       13.91        15.65         3.22        79.00        67.86        70.88 
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        81.83 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        10.78        15.16        63.39        53.26 
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-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
        5.59        23.93        24.95        42.35        44.81        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        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-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       69.93       113.82        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       17.69        31.53        97.48        25.08       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.83        33.99        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        53.98        55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        18.64        23.51         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51        12.59        12.59        12.92        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.33        10.92        11.28         0.16        12.03        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       15.45        16.87         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
       20.88        13.25        20.58        13.48        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        55.50        15.78        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        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        55.30        15.85        16.31        16.64        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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       12.26        33.37        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
       43.00        34.42        27.52        46.59        40.41        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-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 
       38.60        75.98        43.33        32.02        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       69.96        23.24        19.43        21.04        23.87        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        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-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        76.57        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       75.81        28.90       106.75       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56        30.61        34.92        38.76        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        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-A1RD 
        3.02        11.15        48.23        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.72        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56        12.33         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
       32.91        30.18        30.44        23.84        26.70        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       26.40        27.85        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 
       29.85        40.41        41.13        39.78        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90         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-EW-A6S9 
       22.09        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        70.85        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-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-A7W5 TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.62        32.75        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       22.26        16.08         7.46        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        34.92        36.36        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        20.38        26.70        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-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG 
       47.01        64.21        86.96         0.16         0.26        18.48 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       21.07        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        66.84        29.03        15.35        16.04 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           281.29            282.90 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           28.485            28.210 
[1] "0.0 - 281.3 (28.5)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         9        8        2        2        56        27
  XQ GAIN WILD-TYPE      80       75        4        4       296       226
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  XQ GAIN MUTATED           0         17          4          8        4       0
  XQ GAIN WILD-TYPE         2        138         23         57       16      13
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 8                75
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               56               296
  STAGE IIB               27               226
  STAGE III                0                 2
  STAGE IIIA              17               138
  STAGE IIIB               4                23
  STAGE IIIC               8                57
  STAGE IV                 4                16
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    29  90  14   4
  XQ GAIN WILD-TYPE 245 535 123  36
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              29               245
  T2              90               535
  T3              14               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
  XQ GAIN MUTATED    70  40  16  10
  XQ GAIN WILD-TYPE 436 318 103  67
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              70               436
  N1              40               318
  N2              16               103
  N3              10                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"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   117   5
  XQ GAIN WILD-TYPE 772  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    117    5
  XQ GAIN WILD-TYPE  772   17
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0             117               772
  1               5                17
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   136   1
  XQ GAIN WILD-TYPE 931  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    136    1
  XQ GAIN WILD-TYPE  931   11
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE             136               931
  MALE                 1                11
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    53  73
  XQ GAIN WILD-TYPE 384 474
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     53   73
  XQ GAIN WILD-TYPE  384  474
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               53               384
  YES              73               474
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ GAIN MUTATED                            1                           113
  XQ GAIN WILD-TYPE                          0                           655
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ GAIN MUTATED                                9                   3
  XQ GAIN WILD-TYPE                            192                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ GAIN MUTATED                       1                                2
  XQ GAIN WILD-TYPE                     8                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  XQ GAIN MUTATED                    2              5
  XQ GAIN WILD-TYPE                 15             41
D41V9, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                113               655
  INFILTRATING LOBULAR CARCINOMA                 9               192
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                28
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 5                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"
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                          32    81
  XQ GAIN WILD-TYPE                       149   663
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                     32               149
  WHITE                                         81               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"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3 107
  XQ GAIN WILD-TYPE  36 767
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3  107
  XQ GAIN WILD-TYPE   36  767
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             107               767
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   178  45
  1P LOSS WILD-TYPE 739 103
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              223               842 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               45               103 
$`1P LOSS MUTATED`
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09C TCGA-AO-A0JI 
       53.06        29.03        15.06        33.01         1.02        50.24 
TCGA-AQ-A0Y5 TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A1LG 
        5.65        66.15        81.63        10.42        21.14        50.07 
TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-5T-A9QA 
       26.99        52.96        52.96       108.07       131.67         9.96 
TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EN 
       39.32       121.94        77.19       107.93        25.22       134.40 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0T4 
       80.28        79.76        35.05        63.29        27.12        20.52 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX 
       18.21        50.47        21.90        21.67        17.36        60.72 
TCGA-A2-A25C TCGA-A2-A3KC TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DC 
       17.19        36.23        29.98        21.90        30.61        29.79 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       14.73        12.10        13.02        17.03         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08J 
       18.97        18.97        32.05         8.98        38.01        37.05 
TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09N 
       31.00        30.97         9.99        12.00        50.04         1.02 
TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
       25.02        14.01        19.04        21.04        27.02        17.03 
TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FE TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3EH 
       22.95        73.05        86.66        26.04        32.45         6.48 
TCGA-AC-A5EH TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
       16.80        20.19         0.33         0.33         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XP 
        2.96         0.33         6.44         7.00         7.17         0.30 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J5 
        0.33         0.33        80.28        66.77        95.70        26.04 
TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A12A TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       20.32        21.53       102.31        97.08        61.87        11.51 
TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AW TCGA-AR-A24R 
       98.33        83.87       134.14        93.90        86.53       112.77 
TCGA-AR-A24T TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN 
      105.27        89.00        85.64        54.21        39.39        33.30 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RL 
       11.90       129.57       146.50       233.62       165.76        81.17 
TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      162.05       100.70        79.46        18.35        21.01       113.79 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0B5 
      101.52        73.51       139.17        74.99       103.63        70.22 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 
       37.22        43.53        21.70        49.94        41.75        46.39 
TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 
       14.30        81.83        24.49        30.35        10.78        23.08 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P 
       12.89        51.32        32.91        90.84        26.66        30.28 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F8 
        7.36        51.39        69.93        42.28        12.00        25.08 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T 
      114.15        74.73        45.63        83.31       130.16        10.52 
TCGA-BH-A5J0 TCGA-C8-A12W TCGA-C8-A138 TCGA-C8-A1HK TCGA-C8-A26X TCGA-C8-A26Z 
       23.51        12.66        12.49        12.03        12.36        15.45 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-D8-A142 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       24.56        33.99        13.97        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XQ TCGA-D8-A1XR 
       20.09        19.40        15.22        14.73        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I 
       16.31        12.99        15.16         9.93        14.14        14.43 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A15R 
       16.18        12.66        28.44        44.68        34.26        56.94 
TCGA-E2-A1IH TCGA-E2-A576 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NI TCGA-E9-A1R3 
       33.73        34.29        36.56        41.62         9.86         2.56 
TCGA-E9-A1R5 TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A295 
        3.02        21.27        39.09        41.72        38.99        12.33 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OY 
       29.72        38.07        26.70        26.40        28.77        29.85 
TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW 
       23.11         6.15        10.52        19.96        55.00        22.09 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A3NW TCGA-HN-A2NL TCGA-LL-A5YM TCGA-LL-A6FP 
       33.21         7.40       110.50         2.60        15.32        22.26 
TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-OL-A66N TCGA-PL-A8LX TCGA-S3-A6ZF 
       17.49         2.10        22.32        26.04         0.16        18.81 
TCGA-WT-AB44 
       29.03 

$`1P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A07E TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I 
       19.99        33.01        33.01        17.95        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         2.56        32.91        19.20        98.33        17.23 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       57.27        73.35        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-EW-A1J5 
        9.70        14.79        50.79        16.47        73.64        15.68 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       14.79        14.50        40.08        18.87        13.94        11.41 
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD 
      133.05        48.46        47.61        11.44         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ 
       43.43        48.10        14.27        47.24        20.88        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       31.79         7.96        28.01        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       78.41        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CT 
       99.12        24.79       114.81        92.48       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-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU 
       61.58       101.72       118.45        74.40        72.00        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW 
       31.82        61.94        24.72        99.19        54.64        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-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YI 
       17.46        18.90        20.75        32.55        25.28        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-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       22.45        20.25        19.20        16.47        52.47        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15       105.34        10.59        39.65        33.93        91.07 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-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-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
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-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A6VV 
       13.74        14.50        21.17        17.92        10.72        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-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A07J 
       31.00        26.01         1.02        53.98        14.01        12.00 
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-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 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-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09M TCGA-A8-A09R 
       40.01        41.98        12.00         9.99        33.07         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 
       19.04        15.02         0.99        12.00        13.02         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       38.04        19.23        73.91         5.72        22.26        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       19.33        14.66        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        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-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         7.46 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.16         0.33         0.33         5.65         7.96         7.59 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT 
        0.33         5.36         0.33        12.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        61.35        81.63        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       58.95        44.42        32.78        21.40        52.18        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-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       65.10        26.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D 
      113.62       108.72       106.78       108.03        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       70.42        60.56        53.88        40.57        20.45        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH 
       55.86       107.24        65.36       133.22       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY 
       99.32        37.81        94.29        61.28        86.43        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       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        2.76       104.28        97.84       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 
       98.76        98.66        99.62        93.30        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
      166.42        20.25        86.53        63.62        38.17        40.54 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       38.96        10.59        77.62       143.38       281.29       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.52       112.37        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       263.28       102.77       140.28        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      169.51        97.48       188.68       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A3ZX 
       28.27        68.94        58.55        43.59       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        68.12        18.84        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       39.16        84.13        51.68        32.02        18.21        61.51 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       85.87        77.75        77.95        74.14        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        63.32        15.16        63.39        53.26        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-A0W3 
       13.61        36.85        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         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       20.12        72.56        37.74        55.63        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16        91.99       113.82        82.85        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FD 
       17.69        25.81        31.53        97.48       120.62        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.83        33.99        63.35        55.00        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O 
       55.50        28.14        26.14        38.60        57.83        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
       36.79        20.12       110.60        20.88        18.64         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        5.26        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-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56        12.16        13.51        12.59 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.92        12.46        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.28         0.16        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.53        12.95        16.87        16.70         0.03         9.76 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        12.95        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 
       56.81        20.88        13.25        20.58        14.17        13.48 
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        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       18.15        53.00        14.01        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-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        21.83        14.50        19.92        17.69        55.30 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       16.64        43.04        16.54        15.32        15.52        14.24 
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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48        17.06         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73X TCGA-E2-A105 
       12.26        33.37        18.51        21.67        25.22        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-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-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       11.05        19.56        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       38.76        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       34.16        36.20        39.55        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 
       18.94        24.82        28.27        34.95         6.12        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       37.74        38.37        41.03        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 
        0.69         1.94         7.13        24.56         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO 
       30.18        30.44        23.90        23.84         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        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-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        34.03        17.49        17.52        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        24.99        31.30       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      115.69       106.06       101.62        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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.70        14.47         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        19.53        12.36        19.59        27.91        22.39 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        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-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-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-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.48        21.07        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 
       17.39        17.26        17.03         3.81        66.84        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           233.62            282.90 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            26.70             28.47 
[1] "0.2 - 233.6 (26.7)" "0.0 - 282.9 (28.5)"
[1] "hr=" "1.6"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED        13       15        0        1        69        46
  1P LOSS WILD-TYPE      76       68        6        5       283       207
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  1P LOSS MUTATED           1         40         13         18        7       3
  1P LOSS WILD-TYPE         1        115         14         47       13      10
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 13                76
  STAGE IA                15                68
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               69               283
  STAGE IIB               46               207
  STAGE III                1                 1
  STAGE IIIA              40               115
  STAGE IIIB              13                14
  STAGE IIIC              18                47
  STAGE IV                 7                13
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    49 130  30  17
  1P LOSS WILD-TYPE 225 495 107  23
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              49               225
  T2             130               495
  T3              30               107
  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
  1P LOSS MUTATED    86  80  32  22
  1P LOSS WILD-TYPE 420 278  87  55
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              86               420
  N1              80               278
  N2              32                87
  N3              22                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   188   7
  1P LOSS WILD-TYPE 701  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    188    7
  1P LOSS WILD-TYPE  701   15
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0             188               701
  1               7                15
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   224   2
  1P LOSS WILD-TYPE 843  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    224    2
  1P LOSS WILD-TYPE  843   10
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE             224               843
  MALE                 2                10
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    85 115
  1P LOSS WILD-TYPE 352 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     85  115
  1P LOSS WILD-TYPE  352  432
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               85               352
  YES             115               432
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P LOSS MUTATED                            1                           168
  1P LOSS WILD-TYPE                          0                           600
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P LOSS MUTATED                               42                   2
  1P LOSS WILD-TYPE                            159                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P LOSS MUTATED                       0                                3
  1P LOSS WILD-TYPE                     9                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  1P LOSS MUTATED                    2              8
  1P LOSS WILD-TYPE                 15             38
D42V9, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                168               600
  INFILTRATING LOBULAR CARCINOMA                42               159
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 8                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"
D42V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    10
  1P LOSS WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          38   146
  1P LOSS WILD-TYPE                       143   598
D42V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     38               143
  WHITE                                        146               598
[1] 4 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     7 171
  1P LOSS WILD-TYPE  32 703
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7  171
  1P LOSS WILD-TYPE   32  703
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             171               703
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    37  10
  1Q LOSS WILD-TYPE 880 138
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47              1018 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               138 
$`1Q LOSS MUTATED`
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A08S TCGA-BH-A0B6 TCGA-A2-A0CW TCGA-A2-A0YE 
       53.06        29.03        33.01        81.63       107.93        18.21 
TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4S3 TCGA-A7-A0DC TCGA-A8-A079 
       50.47        17.36        60.72        21.90        29.79         9.01 
TCGA-A8-A07L TCGA-A8-A08J TCGA-A8-A09N TCGA-AC-A3BB TCGA-AN-A04A TCGA-AN-A0AR 
       32.05        37.05         1.02        32.45         2.96         0.33 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A1KP TCGA-AO-A1KS 
        0.33         0.33        66.77        95.70        97.08        11.51 
TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A24T TCGA-B6-A0IG TCGA-B6-A0RL TCGA-BH-A0BV 
       98.33        83.87       105.27       146.50        81.17        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-E2-A15R 
       83.31        10.52        12.49        24.56        16.41        56.94 
TCGA-E9-A1ND TCGA-EW-A1J6 TCGA-EW-A6SD TCGA-HN-A2NL TCGA-OL-A5RZ 
       41.62        28.77        33.21         2.60        22.32 

$`1Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       49.05        45.07        29.98        16.57        19.79        14.53 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       19.33        13.71        50.24        17.79         5.65         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
       32.91        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       73.35        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
      133.05       131.67        48.46        47.61        11.44         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-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48       107.93        77.19        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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-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-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G 
       33.11        31.73        20.19        25.15        29.56        23.74 
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-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-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G 
        1.02        17.03        53.98        43.00        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       14.01        12.00         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-A08I TCGA-A8-A08L 
        0.99        38.01        28.96        19.96        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99       112.08        43.00        40.01 
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-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        33.07        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        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       33.04        19.33        14.66         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       24.79        29.26        16.80        14.96        11.44        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-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-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         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         6.90 
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 
        5.36         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 
       69.83        58.95        44.42        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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03       102.31        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR 
       60.56        53.88        40.57        20.45        61.87        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       24.79        26.93       130.09        15.62        32.52       140.55 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        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       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      125.16       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       86.53        86.43        33.73       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84       102.84       105.30        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       89.00        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        11.90       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.52       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       282.90       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.46        18.35        21.01       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.55        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       73.51       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       74.99        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        74.14        41.75        46.39        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 
       81.83        24.49        31.00        63.32        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        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-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        32.91         4.90        35.93        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-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-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62        33.17       122.83        33.99        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        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      110.60        20.88        18.64        23.51         9.63         5.26 
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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56        12.16        13.51        12.59 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.92        12.46        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        12.03        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       20.25        12.53        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
       16.70         0.03         9.76        14.43        33.99        12.95 
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        56.81        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-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        55.50        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        53.00        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        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48        17.06         1.61        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 
       12.66        25.22        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        75.98 
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        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       11.05        19.56        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       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        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        22.29        34.16        36.20        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV 
        8.48        18.21        18.90        13.25        16.57        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-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-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        17.52        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30         7.40       109.87        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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
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-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       16.08        15.68         7.46        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        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-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-AA0Z TCGA-S3-AA10 
        9.93        18.81        18.48        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.33              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            146.5             282.9 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            32.45             27.55 
[1] "0.3 - 146.5 (32.5)" "0.0 - 282.9 (27.5)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         3        3        0        0        14        13
  1Q LOSS WILD-TYPE      86       80        6        6       338       240
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  1Q LOSS MUTATED           0         11          1          2        1       0
  1Q LOSS WILD-TYPE         2        144         26         63       19      13
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 3                80
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               14               338
  STAGE IIB               13               240
  STAGE III                0                 2
  STAGE IIIA              11               144
  STAGE IIIB               1                26
  STAGE IIIC               2                63
  STAGE IV                 1                19
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    11  28   7   2
  1Q LOSS WILD-TYPE 263 597 130  38
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              11               263
  T2              28               597
  T3               7               130
  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
  1Q LOSS MUTATED    14  22   8   4
  1Q LOSS WILD-TYPE 492 336 111  73
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              14               492
  N1              22               336
  N2               8               111
  N3               4                73
[1] 4 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    45   1
  1Q LOSS WILD-TYPE 844  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     45    1
  1Q LOSS WILD-TYPE  844   21
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              45               844
  1               1                21
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                   0    1
  1Q LOSS MUTATED     48    0
  1Q LOSS WILD-TYPE 1019   12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     48    0
  1Q LOSS WILD-TYPE 1019   12
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              48              1019
  MALE                 0                12
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    20  20
  1Q LOSS WILD-TYPE 417 527
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     20   20
  1Q LOSS WILD-TYPE  417  527
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               20               417
  YES              20               527
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q LOSS MUTATED                            0                            42
  1Q LOSS WILD-TYPE                          1                           726
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q LOSS MUTATED                                5                   1
  1Q LOSS WILD-TYPE                            196                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q LOSS MUTATED                       0                                0
  1Q LOSS WILD-TYPE                     9                               30
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  1Q LOSS MUTATED                    0              0
  1Q LOSS WILD-TYPE                 17             46
D43V9, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 42               726
  INFILTRATING LOBULAR CARCINOMA                 5               196
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                30
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 0                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"
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                          10    26
  1Q LOSS WILD-TYPE                       171   718
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                     10               171
  WHITE                                         26               718
[1] 4 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     2  31
  1Q LOSS WILD-TYPE  37 843
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   31
  1Q LOSS WILD-TYPE   37  843
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO              31               843
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED   157  24
  2P LOSS WILD-TYPE 760 124
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              181               884 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               124 
$`2P LOSS MUTATED`
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09C TCGA-AO-A0JI 
       22.32        11.28        33.01        33.01         1.02        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A1AM TCGA-D8-A146 TCGA-E2-A2P5 
       17.79         5.65        32.91        98.33        21.14        26.99 
TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0EO 
      133.05        11.44        77.19        75.25        98.99        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0T7 TCGA-A2-A0YH TCGA-A2-A1FW 
       35.05        34.29        27.12        20.75        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13F 
       60.72        42.44        24.39        35.31        29.79        25.15 
TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F 
       10.42        13.02        26.01         1.02        43.00        18.97 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08O 
       10.98         8.98         9.99        38.01        37.05        31.00 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 
       30.97        12.00         1.02        25.02        19.04        19.04 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FF 
       21.04        27.02        17.03        22.95        99.35        90.71 
TCGA-AC-A2FM TCGA-AC-A3EH TCGA-AC-A62V TCGA-AC-A7VC TCGA-AN-A03Y TCGA-AN-A0AJ 
       26.04         6.48        11.44         0.03         0.33         9.96 
TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ 
        0.33         7.00         7.59         7.04         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 
        0.30         0.33        80.28        61.35        95.70        21.40 
TCGA-AO-A12A TCGA-AO-A1KS TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AN TCGA-AR-A1AS 
      102.31        11.51       107.24       134.14        96.00        37.81 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK 
      160.90        50.89       112.77       105.30        50.96        54.21 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 
      112.37       233.62        81.17        43.59        73.51        68.12 
TCGA-BH-A0BA TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 
       37.22        77.75        49.94        90.97         4.41        14.30 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU 
       24.49        31.00        23.08        41.00        52.96        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES 
       51.32        27.25        50.79        35.93        55.63       113.82 
TCGA-BH-A1EU TCGA-BH-A1FN TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X 
       42.28        72.07        23.51         5.26        12.66        12.66 
TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1JD 
       12.49        11.34        33.99        56.81        13.97        18.15 
TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ 
       18.97        21.01        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-A14Z TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G 
       44.68        38.60        18.51        69.96        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN 
       12.92        14.07        76.57        37.25        33.73        22.19 
TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
       32.88        22.29        35.24        11.15        45.01        32.09 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G 
       46.65        21.27        47.64        42.25        41.03        40.73 
TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 
        7.13        38.07        30.44        23.84        26.40        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE 
       28.77        22.82        29.85        23.11         7.86        10.52 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-GI-A2C8 
       25.91        22.09        17.52        15.22        16.77         7.40 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH 
       16.08        15.68        19.53        64.21         0.16        21.07 
TCGA-XX-A89A 
       16.04 

$`2P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       23.80        21.73        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I 
       19.99        15.06        33.01        17.95        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
        2.56        19.20        17.23        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG 
       10.42        14.79        50.79        16.47        73.64        50.07 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       29.23        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ 
       13.94        11.41        52.96       108.07       131.67        48.46 
TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       47.61         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
      121.94        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU 
       99.12        24.79       114.81        92.48       107.93         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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       25.22       101.72       134.40       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       72.00        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        44.88        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-A0YC 
        8.38        49.84        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        18.21        50.47        21.90        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ 
       19.33        48.46        31.73        23.77        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D 
       20.25        19.20        16.47        52.47        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        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       50.83         7.30        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       21.90        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       33.11        31.73        20.19        29.56        23.74        20.61 
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-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-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        10.29         9.37         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G 
       17.98        31.00        17.03        53.98         9.01        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U 
       14.01        12.00        32.05         9.99         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-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       19.96        12.00         9.99        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        41.98        12.00         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       50.04        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        19.23        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG 
        5.72        22.26        73.05        40.57        86.66        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
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-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 
       20.19         1.12         1.32         2.30         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY 
        7.96         7.17         6.90         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XU 
        5.36         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        66.77        81.63        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        44.42        32.78        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-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        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       115.27       113.62       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        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        61.87        82.62        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
      130.09        15.62        32.52       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22        83.87       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      101.00       103.86        97.68        86.07        93.90        99.32 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       94.29        61.28        86.53        86.43        33.73        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      105.27       102.84        98.76        98.66        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       93.30        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       86.53        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
      275.87       129.57        50.70        65.52       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
      101.52       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       74.99        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        51.68        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       74.14        76.60        85.87        77.95        74.14        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       46.39        89.06        81.73        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       79.00        67.86        70.88        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        81.83        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       63.39        53.26        24.56        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
        2.50        13.61        36.85         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        32.91         4.90        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-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        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-A42T 
       57.83       130.16        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-BH-A8G0 
      110.60        20.88        18.64         9.63        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
       13.51        12.59        12.59        12.92        12.46        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.28         0.16        12.03        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Z 
       12.95        13.02        12.49        13.41        19.46        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        14.17        13.48        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        55.50        15.78        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       53.00        14.01        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       20.38        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        55.30        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       16.64        12.99        43.04        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        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       31.96        69.34        63.62        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       23.87        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-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        77.65        37.41        70.36        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       59.18         3.88        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       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        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 
       34.92        38.76        34.29        17.69        34.82        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD 
        2.56         6.12         3.02        48.23        40.24         1.12 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A 
        6.58        46.59        34.45        32.05        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       38.37        41.72        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        1.94        24.56        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       30.18        23.90        26.70         0.79        25.81        27.85 
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-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       25.94        29.95        40.41        41.13        39.78        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-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 
       14.43        34.55        19.96        55.00        52.73        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 
       17.49        23.51        24.99        31.30        33.21       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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        62.47        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7T0 
       14.70        14.47        22.26         2.63         7.46        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        34.92        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-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-A5DE TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       17.39        17.26        17.03         3.81        66.84        29.03 
TCGA-XX-A899 TCGA-Z7-A8R6 
       15.35       107.05 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.03              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           233.62            282.90 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            24.49             29.13 
[1] "0.0 - 233.6 (24.5)" "0.0 - 282.9 (29.1)"
[1] "hr=" "1.2"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED        11       13        0        1        56        40
  2P LOSS WILD-TYPE      78       70        6        5       296       213
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  2P LOSS MUTATED           1         32          6         14        7       3
  2P LOSS WILD-TYPE         1        123         21         51       13      10
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 11                78
  STAGE IA                13                70
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               56               296
  STAGE IIB               40               213
  STAGE III                1                 1
  STAGE IIIA              32               123
  STAGE IIIB               6                21
  STAGE IIIC              14                51
  STAGE IV                 7                13
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    39 111  24   9
  2P LOSS WILD-TYPE 235 514 113  31
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              39               235
  T2             111               514
  T3              24               113
  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    83  53  29  17
  2P LOSS WILD-TYPE 423 305  90  60
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              83               423
  N1              53               305
  N2              29                90
  N3              17                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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   146   8
  2P LOSS WILD-TYPE 743  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    146    8
  2P LOSS WILD-TYPE  743   14
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0             146               743
  1               8                14
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   181   3
  2P LOSS WILD-TYPE 886   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    181    3
  2P LOSS WILD-TYPE  886    9
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE             181               886
  MALE                 3                 9
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    73  97
  2P LOSS WILD-TYPE 364 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     73   97
  2P LOSS WILD-TYPE  364  450
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               73               364
  YES              97               450
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P LOSS MUTATED                            0                           143
  2P LOSS WILD-TYPE                          1                           625
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P LOSS MUTATED                               25                   0
  2P LOSS WILD-TYPE                            176                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P LOSS MUTATED                       3                                6
  2P LOSS WILD-TYPE                     6                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  2P LOSS MUTATED                    2              5
  2P LOSS WILD-TYPE                 15             41
D44V9, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                143               625
  INFILTRATING LOBULAR CARCINOMA                25               176
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 5                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"
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                          22   125
  2P LOSS WILD-TYPE                       159   619
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                     22               159
  WHITE                                        125               619
[1] 4 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    10 133
  2P LOSS WILD-TYPE  29 741
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10  133
  2P LOSS WILD-TYPE   29  741
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                29
  NOT HISPANIC OR LATINO             133               741
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED   177  30
  2Q LOSS WILD-TYPE 740 118
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              207               858 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               118 
$`2Q LOSS MUTATED`
TCGA-A7-A3J1 TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09C TCGA-AO-A0JI 
       11.28        53.06        33.01        33.01         1.02        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-D8-A146 
       17.79         5.65         2.56        32.91        98.33        21.14 
TCGA-E2-A2P5 TCGA-3C-AAAU TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT 
       26.99       133.05        48.46        11.44        77.19        75.25 
TCGA-A2-A0CV TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0T7 
       98.99        80.28        35.05        34.29        27.12        20.75 
TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CE 
       21.67        17.36        60.72        33.93        24.39        35.31 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Y 
       29.79        20.19        25.15        10.42        13.02        26.01 
TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W 
        1.02        43.00        18.97        10.98         8.98         9.99 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A092 TCGA-A8-A09B 
       38.01        12.00        37.05        31.00        30.97        12.00 
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-A3EH 
       17.03        22.95        99.35        90.71        26.04         6.48 
TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS 
       11.44        13.58         0.03         0.33         9.96         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        7.00         7.59         7.04         0.36         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 
        0.30         0.33        80.28        61.35        95.70        21.40 
TCGA-AO-A0JD TCGA-AO-A12A TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U3 
       72.00       102.31        11.51        84.10        75.22       134.14 
TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R 
       96.00        37.81        33.73       160.90        50.89       112.77 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ 
      105.30        50.96        54.21        11.90       112.37       233.62 
TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 
       81.17       282.90        43.59        73.51       139.17        68.12 
TCGA-BH-A0BA TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 
       37.22        77.75        49.94        90.97         4.41        14.30 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU 
       24.49        31.00        23.08        41.00        52.96        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU 
       51.32        27.25        35.93        55.63       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       12.00        97.48       114.15        45.63        72.07        26.14 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 
       18.64        23.51         5.26        12.66        12.66        12.49 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A3M7 TCGA-D8-A13Y 
       10.92        11.34        12.03        15.45        33.99        56.81 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A1JI TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       20.88        13.97        18.97        17.79        27.58        18.15 
TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       21.83        15.85        15.16        16.54         9.93        14.14 
TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 
       13.08        44.68        38.60        31.96        18.51        69.96 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1BD 
       20.71        18.21        12.92        14.07        76.57        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NF 
       33.73        33.70        22.19        32.88        22.29        35.24 
TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RG 
        9.86        11.15        45.01        32.09        46.65        21.27 
TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A249 TCGA-E9-A3HO 
       47.64        42.25        41.03        40.73         7.13        38.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW 
       30.44        23.84        26.40        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-EW-A6S9 TCGA-GM-A2DF TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-LL-A6FR 
       17.52        15.22        70.85        72.03         2.60        16.08 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A6VO TCGA-PE-A5DD TCGA-PL-A8LX 
       19.53        12.36        22.32        28.21        64.21         0.16 
TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
       21.07        17.39        16.04 

$`2Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        21.73        22.32        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I 
       19.99        15.06        33.01        17.95        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AQ-A7U7 TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 
       19.20        17.23        66.15        57.27        73.35        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 
       14.79        50.79        16.47        73.64        50.07        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALK TCGA-5T-A9QA 
       11.41        52.96       108.07       131.67        47.61         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-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
      114.81        92.48       107.93         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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV 
      134.40       118.45        79.76        74.40        72.00        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW 
       61.94        24.72        63.29        99.19        54.64        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-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-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-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        22.45        20.25        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG 
       21.30        23.21        26.96        21.14        21.90        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-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        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-A6VV TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 
        8.75        13.02         1.02        17.98        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       53.98         9.01        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 
        9.99         7.99        24.99        45.07        18.05        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08P 
       13.02         0.99        28.96        19.96         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 
        0.99       112.08        43.00        40.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V 
        9.99         9.99        50.04        33.07         8.98        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD 
        0.99        14.01        12.00        13.02         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       19.23        73.91         5.72        22.26        73.05        40.57 
TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       86.66        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       14.66        32.45        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
       16.80        14.96        17.42        18.67        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         7.46         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-A0FY 
        5.65         7.96         7.17         6.90         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XU 
        5.36         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        66.77        81.63        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        44.42        32.78        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B 
      115.27       113.62       108.72       106.78       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       82.68        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       97.08        61.87        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
       15.62        32.52       140.55        98.33         5.26       109.02 
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       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       83.87       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AV 
       97.68        86.07        93.90        99.32        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       86.53        86.43        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        2.76       104.28        97.84       105.27       102.84        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.66        89.00        99.62        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       255.68        68.45       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      169.51        97.48       188.68        79.46        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       58.55       101.52       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       74.99        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        51.68        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       74.14        76.60        85.87        77.95        74.14        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       46.39        89.06        81.73        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       79.00        67.86        70.88        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        81.83        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       63.39        53.26        24.56        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
        2.50        13.61        36.85        50.79         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        32.91         4.90 
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-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       91.99        82.85        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       31.53        25.08       120.62        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       33.99        63.35        55.00        53.98        55.50        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A8FZ 
       20.12        10.52       110.60        20.88         9.63        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-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.16        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       12.33        11.28         0.16        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.36        12.95        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        24.56        14.43        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       12.49        13.41        19.46        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        55.50 
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        53.00        14.01 
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-A1X7 TCGA-D8-A1X8 
       12.20        13.32        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-A1XK 
       23.90        12.39        17.16        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69        55.30        16.41        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.99        43.04        15.32        15.52        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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       13.48        17.06         1.61        10.09        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        12.66        25.22 
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-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y 
       33.17        75.98        43.33        34.26        32.02        69.34 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       63.62        23.24        19.43        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
        9.04        20.58        11.05        19.56        56.94        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE 
       53.62        87.22        33.01        32.35        28.50        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       37.41        70.36        28.44        59.18         3.88        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       43.56         8.28        30.61        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       17.69        34.82        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       39.55        41.62        35.77        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       28.27        34.95         2.56         6.12         3.02        48.23 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         1.12         6.58        46.59        34.45        32.05 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.69        38.99         1.94        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
        9.47        32.91        30.18        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       13.25        16.57        25.94        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       39.78        29.82        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB 
       52.73        34.03        17.49        23.51        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        83.34        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       21.24         7.10        13.28        10.62        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       15.32        14.70        14.47        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        7.46        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        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-AA15 
       18.81        18.48        20.68        19.27        13.84        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       17.03         3.81        66.84        29.03        15.35       107.05 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           282.90            281.29 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            25.15             29.13 
[1] "0.0 - 282.9 (25.1)" "0.0 - 281.3 (29.1)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED        13       14        0        1        66        44
  2Q LOSS WILD-TYPE      76       69        6        5       286       209
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  2Q LOSS MUTATED           1         36          7         15        8       3
  2Q LOSS WILD-TYPE         1        119         20         50       12      10
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 13                76
  STAGE IA                14                69
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               66               286
  STAGE IIB               44               209
  STAGE III                1                 1
  STAGE IIIA              36               119
  STAGE IIIB               7                20
  STAGE IIIC              15                50
  STAGE IV                 8                12
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    45 124  29  11
  2Q LOSS WILD-TYPE 229 501 108  29
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              45               229
  T2             124               501
  T3              29               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
  2Q LOSS MUTATED    94  63  32  18
  2Q LOSS WILD-TYPE 412 295  87  59
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              94               412
  N1              63               295
  N2              32                87
  N3              18                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"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   169   8
  2Q LOSS WILD-TYPE 720  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    169    8
  2Q LOSS WILD-TYPE  720   14
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0             169               720
  1               8                14
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   208   2
  2Q LOSS WILD-TYPE 859  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    208    2
  2Q LOSS WILD-TYPE  859   10
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE             208               859
  MALE                 2                10
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    84 109
  2Q LOSS WILD-TYPE 353 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     84  109
  2Q LOSS WILD-TYPE  353  438
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               84               353
  YES             109               438
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q LOSS MUTATED                            0                           163
  2Q LOSS WILD-TYPE                          1                           605
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q LOSS MUTATED                               27                   2
  2Q LOSS WILD-TYPE                            174                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q LOSS MUTATED                       3                                7
  2Q LOSS WILD-TYPE                     6                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  2Q LOSS MUTATED                    2              6
  2Q LOSS WILD-TYPE                 15             40
D45V9, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                163               605
  INFILTRATING LOBULAR CARCINOMA                27               174
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 6                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"
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                          31   136
  2Q LOSS WILD-TYPE                       150   608
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                     31               150
  WHITE                                        136               608
[1] 4 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    11 154
  2Q LOSS WILD-TYPE  28 720
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11  154
  2Q LOSS WILD-TYPE   28  720
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             154               720
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   156  30
  3P LOSS WILD-TYPE 761 118
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              186               879 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               118 
$`3P LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26F TCGA-A7-A2KD TCGA-A8-A06U TCGA-Z7-A8R5 TCGA-3C-AAAU 
       19.20        24.26        22.32        29.03       108.07       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL 
      131.67        48.46        31.79        73.84        87.25        99.12 
TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
       75.25       107.93        56.81        67.33        34.55        25.22 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YT TCGA-A2-A1G1 
       80.28        79.76        49.84        18.21        23.77        19.20 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A13D 
       47.31        35.93        26.96        35.31        30.61        31.73 
TCGA-A7-A4SF TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06R TCGA-A8-A06Z 
       17.92         9.37        10.42         8.75        17.98         1.02 
TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A08O TCGA-A8-A09M TCGA-AC-A2BK TCGA-AC-A2FO 
       18.97        12.00        31.00        33.07        73.05        74.14 
TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AR 
       14.83         1.12         0.23         1.78         1.71         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M 
        7.96         7.59         7.04         0.33        80.28        61.35 
TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A124 
       95.70        69.83        21.40        21.53        26.24       115.27 
TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U1 
       11.51       130.09       140.55       109.02        64.83       133.22 
TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A251 
       83.87       125.16        99.32        97.84       105.27        99.62 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH 
       71.05        93.83        39.39       129.57       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A409 
      233.62        97.48        18.35       113.79        73.51        18.84 
TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       51.68        61.51        21.70        77.95        74.14        46.39 
TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW 
       29.98        78.28         4.41        52.96        12.89        51.32 
TCGA-BH-A0RX TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 
        5.59        32.91        26.66         7.36        69.93        25.08 
TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12P 
       45.63        55.50        57.83        10.52        18.64        11.77 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.92        12.46        10.92        11.34         0.16        12.03 
TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-D8-A1J8 TCGA-D8-A1J9 
       12.33        12.53        13.02        12.49        14.17        17.49 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 
       18.15        53.00        20.09        20.12        19.40        18.58 
TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XT TCGA-D8-A1XU 
       18.15        21.83        14.50        19.92        16.64        12.99 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A27N TCGA-E2-A10C 
       16.54        15.32         9.93        13.48        17.06        40.11 
TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A 
       38.60        34.26        63.62        69.96        25.05        23.34 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A574 TCGA-E2-A576 
       33.70        60.99        60.36        28.90        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A226 
       17.69        34.16        39.55        35.24         6.12        34.45 
TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1OW 
       37.74        40.73         0.69        12.33        29.72        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6S9 
       29.82        23.11         6.15        52.73        17.52        15.22 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX 
        7.40       109.87        79.10        72.10         2.60        11.57 
TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RY TCGA-OL-A66K 
        7.10        17.06        12.36        19.59        24.72        41.92 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-V7-A7HQ TCGA-XX-A89A 
       26.04        18.48        21.07        19.27        66.84        16.04 

$`3P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        31.36        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        11.05        53.06        19.99        15.06 
TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       33.01        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       45.07        29.98        16.57        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       13.71        50.24        17.79         5.65         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       19.20        98.33        17.23        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AALK 
       40.08        18.87        13.94        11.41        52.96        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
      101.98        55.43       136.73        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        77.19         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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       60.72        22.45        20.25        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       33.93        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       21.90        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       29.79        20.19        25.15        29.56        23.74        20.61 
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-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-A6VV TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
       10.29        13.02        13.02         1.02        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98         9.01        43.00        18.97        14.01 
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-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-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45         6.48        16.31        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        17.42        18.67        13.58        12.26 
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-A04A TCGA-AN-A0AJ 
        0.33         0.33         0.33         0.62         2.96         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        5.65         7.00         7.17         6.90         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         5.36         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-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       66.77        81.63        68.75        58.95        44.42        32.78 
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-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JJ 
       50.70        50.86        72.00        76.77        65.10        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      102.31        98.27        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       40.57        20.45        97.08        61.87        82.62        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       26.93        15.62        32.52        98.33         5.26        84.10 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U3 
       75.22        98.93        55.86       107.24        65.36       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        93.90        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.43        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U 
       99.78       118.59         2.76       104.28       112.77       102.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
      105.30        50.96        98.76        98.66        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29        11.90       275.87        50.70        65.52 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ 
      282.90       169.51       188.68        79.46        21.01       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
      101.52       139.17       170.17        37.87         7.07        85.35 
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        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        37.22        32.02        18.21        43.53 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       85.87        77.75        49.94        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DP 
       81.73        77.98        67.10        38.01        13.91        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        79.00        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        23.08        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        27.25        50.79 
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         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       55.63        37.55        66.05        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-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       17.69        25.81        31.53        97.48       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       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       72.07        53.98        28.14        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
      130.16        36.82        36.79        20.12       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI 
       13.51        12.59        12.59        12.49        12.33        11.28 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        12.33        20.25        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       33.99        12.95        13.41        19.46        56.81        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-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH 
       16.50        55.50        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JL 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-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       14.70        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO 
       12.39        17.16        15.22        14.73        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.41        15.85        16.31        15.16        43.04        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-A27P TCGA-D8-A27R TCGA-D8-A27T 
       14.43        48.03        16.41         1.61        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 
       12.66        25.22        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-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W 
       40.96        38.24        33.17        75.98        43.33        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       31.96        69.34        18.51        23.24        19.43        21.04 
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        55.63        53.92         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        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       22.19        11.08        54.18        19.66        24.59        75.81 
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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
        8.28        30.61        34.92        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       22.29        36.20        36.56        41.62        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        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        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       32.05        42.25        39.09        38.37        41.03        41.72 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        26.70         0.79        25.81        26.40        27.85 
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-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        28.77        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       41.13        39.78        18.48        30.08         7.86        18.90 
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-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        25.91        22.09        34.03        17.49        23.51 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        24.99        31.30        33.21        59.57       216.76 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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        62.47        11.84        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       13.28        10.62        32.75        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       22.26         2.63        16.08        15.68         7.46        19.53 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ 
       31.99        58.62        34.92        36.36        28.87        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        18.81 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       20.68        13.84        17.39        17.26        17.03         3.81 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       29.03        15.35       107.05 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.16              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           233.62            282.90 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            26.81             28.27 
[1] "0.2 - 233.6 (26.8)" "0.0 - 282.9 (28.3)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED        11       12        1        0        63        57
  3P LOSS WILD-TYPE      78       71        5        6       289       196
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  3P LOSS MUTATED           0         24          3         11        3       3
  3P LOSS WILD-TYPE         2        131         24         54       17      10
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 11                78
  STAGE IA                12                71
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               63               289
  STAGE IIB               57               196
  STAGE III                0                 2
  STAGE IIIA              24               131
  STAGE IIIB               3                24
  STAGE IIIC              11                54
  STAGE IV                 3                17
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    32 132  20   3
  3P LOSS WILD-TYPE 242 493 117  37
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              32               242
  T2             132               493
  T3              20               117
  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  65  20  13
  3P LOSS WILD-TYPE 419 293  99  64
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              87               419
  N1              65               293
  N2              20                99
  N3              13                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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   152   3
  3P LOSS WILD-TYPE 737  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    152    3
  3P LOSS WILD-TYPE  737   19
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             152               737
  1               3                19
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   188   0
  3P LOSS WILD-TYPE 879  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    188    0
  3P LOSS WILD-TYPE  879   12
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             188               879
  MALE                 0                12
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    64 107
  3P LOSS WILD-TYPE 373 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     64  107
  3P LOSS WILD-TYPE  373  440
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               64               373
  YES             107               440
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P LOSS MUTATED                            0                           154
  3P LOSS WILD-TYPE                          1                           614
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P LOSS MUTATED                               20                   1
  3P LOSS WILD-TYPE                            181                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P LOSS MUTATED                       2                                3
  3P LOSS WILD-TYPE                     7                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  3P LOSS MUTATED                    1              7
  3P LOSS WILD-TYPE                 16             39
D46V9, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                154               614
  INFILTRATING LOBULAR CARCINOMA                20               181
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             1                16
  OTHER, SPECIFY                                 7                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"
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                          42   119
  3P LOSS WILD-TYPE                       139   625
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                     42               139
  WHITE                                        119               625
[1] 4 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     2 165
  3P LOSS WILD-TYPE  37 709
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  165
  3P LOSS WILD-TYPE   37  709
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO             165               709
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    85  19
  3Q LOSS WILD-TYPE 832 129
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              104               961 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               129 
$`3Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26F TCGA-A7-A2KD TCGA-A8-A06U TCGA-Z7-A8R5 TCGA-3C-AAAU 
       19.20        24.26        22.32        29.03       108.07       133.05 
TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX 
       48.46        31.79        73.84        75.25       107.93        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0YE TCGA-A2-A0YT 
       34.55        25.22        80.28        79.76        18.21        23.77 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A4SF TCGA-A7-A6VY TCGA-A8-A06R 
       47.31        35.93        26.96        17.92         8.75        17.98 
TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A08O TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A8OQ 
        1.02        18.97        31.00        74.14        14.83         1.12 
TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0FJ TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03P 
        1.78         0.33         7.96         7.04         0.33        95.70 
TCGA-AO-A0JA TCGA-AO-A124 TCGA-AO-A1KS TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A1AH 
       21.53       115.27        11.51       109.02        83.87       125.16 
TCGA-AR-A1AQ TCGA-AR-A251 TCGA-B6-A0IG TCGA-B6-A1KI TCGA-B6-A409 TCGA-BH-A0B9 
       99.32        99.62       146.50        73.51        18.84        51.68 
TCGA-BH-A0BJ TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18L 
       21.70        74.14        46.39        51.32        32.91        26.66 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12P 
        7.36        69.93        45.63        55.50        57.83        11.77 
TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM TCGA-D8-A1J8 
       12.92        10.92        11.34        12.03        12.33        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XB 
       17.49        18.15        53.00        20.09        19.40        18.15 
TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27N TCGA-E2-A10C 
       16.64        16.54        15.32         9.93        17.06        40.11 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A15A TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A574 
       38.60        75.98        23.34        60.99        60.36        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 
       34.29        17.69         6.12        34.45        40.73         0.69 
TCGA-E9-A247 TCGA-E9-A295 TCGA-EW-A1P5 TCGA-EW-A6S9 TCGA-GI-A2C9 TCGA-JL-A3YX 
       38.99        12.33        23.11        15.22       109.87        11.57 
TCGA-LD-A7W5 TCGA-LL-A7T0 TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG TCGA-S3-AA10 
        7.10        12.36        41.92        26.04        18.48        19.27 
TCGA-V7-A7HQ TCGA-XX-A89A 
       66.84        16.04 

$`3Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        31.36        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        11.05        53.06        19.99        15.06 
TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       33.01        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       45.07        29.98        16.57        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       13.71        50.24        17.79         5.65         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       19.20        98.33        17.23        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AALI 
       40.08        18.87        13.94        11.41        52.96       131.67 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
       24.79       114.81        92.48       107.93        77.19         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 
      118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       22.45        20.25        19.20        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       33.93        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        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-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        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-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        10.29         9.37        10.42 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 
       13.02        13.02         1.02        31.00        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        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-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-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        26.04        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP 
       19.33        14.66        32.45         6.48        16.31        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       29.26        16.80        14.96        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-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         7.46 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.16         0.33         0.33         6.44         5.65         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.59         7.17         6.90         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         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 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-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        81.63        68.75        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        32.78        21.40        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        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 
      113.62       108.72       106.78       108.03       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       82.68        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       97.08        61.87        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      133.22       134.14       107.21       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        86.53        86.43        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       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        89.00        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.52       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       43.59       101.52       139.17       170.17        37.87         7.07 
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        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        84.13        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        85.87        77.75        49.94        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        89.06        90.97        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        79.00        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        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-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         4.90        35.93        20.12        90.84 
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-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        91.99       113.82        82.85        42.28 
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-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        25.08       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.83        33.99        63.35        55.00        72.07        53.98 
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        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       36.79        20.12        10.52       110.60        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       13.51        12.59        12.59        12.46        12.49        12.33 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       11.28         0.16        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        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        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA 
       20.58        13.97        14.17        13.48        19.20        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        18.90        12.03        14.01        18.97 
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-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-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       16.31        12.99        15.16        43.04        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-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       48.03        16.41        13.48         1.61        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 
       12.66        25.22        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-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       40.96        38.24        33.17        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        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       54.18        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       30.61        34.92        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        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        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 
       38.37        41.03        41.72        40.50        20.12         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        7.13        24.56        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        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-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-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       17.52        23.51        16.77        24.99        31.30        33.21 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
        7.40        59.57       216.76        79.10        83.34        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-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-LD-A66U 
       13.55        18.12         2.60        62.47        11.84        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        10.62        32.75        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-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       19.53        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        34.92        36.36 
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-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-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         9.93        18.81        21.07        20.68        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 
       17.39        17.26        17.03         3.81        29.03        15.35 
TCGA-Z7-A8R6 
      107.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.33              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            146.5             282.9 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            24.74             28.44 
[1] "0.3 - 146.5 (24.7)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.5"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        9        0        0        36        33
  3Q LOSS WILD-TYPE      87       74        6        6       316       220
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  3Q LOSS MUTATED           0         16          1          5        2       1
  3Q LOSS WILD-TYPE         2        139         26         60       18      12
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                87
  STAGE IA                 9                74
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               36               316
  STAGE IIB               33               220
  STAGE III                0                 2
  STAGE IIIA              16               139
  STAGE IIIB               1                26
  STAGE IIIC               5                60
  STAGE IV                 2                18
  STAGE X                  1                12
[1] 12  2
[1] TRUE
[1] "dimension of 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    16  78   9   1
  3Q LOSS WILD-TYPE 258 547 128  39
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              16               258
  T2              78               547
  T3               9               128
  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    47  36  14   6
  3Q LOSS WILD-TYPE 459 322 105  71
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              47               459
  N1              36               322
  N2              14               105
  N3               6                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    88   2
  3Q LOSS WILD-TYPE 801  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     88    2
  3Q LOSS WILD-TYPE  801   20
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              88               801
  1               2                20
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   105   0
  3Q LOSS WILD-TYPE 962  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    105    0
  3Q LOSS WILD-TYPE  962   12
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE             105               962
  MALE                 0                12
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    38  55
  3Q LOSS WILD-TYPE 399 492
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     38   55
  3Q LOSS WILD-TYPE  399  492
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               38               399
  YES              55               492
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q LOSS MUTATED                            0                            88
  3Q LOSS WILD-TYPE                          1                           680
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q LOSS MUTATED                               12                   0
  3Q LOSS WILD-TYPE                            189                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q LOSS MUTATED                       1                                1
  3Q LOSS WILD-TYPE                     8                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  3Q LOSS MUTATED                    0              3
  3Q LOSS WILD-TYPE                 17             43
D47V9, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 88               680
  INFILTRATING LOBULAR CARCINOMA                12               189
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 3                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"
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                          23    66
  3Q LOSS WILD-TYPE                       158   678
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                     23               158
  WHITE                                         66               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"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  94
  3Q LOSS WILD-TYPE  39 780
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   94
  3Q LOSS WILD-TYPE   39  780
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO              94               780
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   293  55
  4P LOSS WILD-TYPE 624  93
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              348               717 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               55                93 
$`4P LOSS MUTATED`
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A09C 
       21.73        22.32        53.06        15.06        33.01         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A1KT TCGA-AQ-A0Y5 
       49.05        45.07        19.33        13.71        17.79         5.65 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1L8 TCGA-E2-A1LG 
       98.33        17.23        10.42        14.79        73.64        50.07 
TCGA-LL-A5YP TCGA-S3-AA17 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SI 
       14.79        13.94       133.05       131.67        48.46        20.88 
TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL TCGA-A2-A0CM 
       31.79        39.32        28.01        18.02        99.12        24.79 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0SV 
       77.19        98.99       107.93        67.33        79.76        27.12 
TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A1FW 
       17.13        20.75        18.21        21.67        18.61        17.36 
TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4RW 
       19.20        17.19        33.93        91.07        50.37         7.30 
TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       24.39        35.31        30.61        35.67        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV 
       25.15        23.74        14.50        14.73        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
        9.37        10.42         8.75         1.02        31.00        26.01 
TCGA-A8-A07B TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08I 
       43.00         9.99         8.98        36.95        38.01        12.00 
TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09X TCGA-AC-A23C 
        9.99         0.99        43.00        30.97        14.01        19.23 
TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A5EH 
       22.95        73.05        19.33        32.45         6.48        16.80 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 
       11.44        17.42        13.58         0.03         1.12         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM 
        0.33         0.62         2.96         1.71         9.96         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-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XO 
        7.04         0.33         0.36         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03N 
        0.30         0.33         0.33         0.33         5.59        66.77 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A0JM 
       32.78        21.40        52.18        20.32        76.77        71.80 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ 
      115.27       108.03       102.31        82.68        60.56        61.87 
TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TY 
       11.51        26.93       130.09       140.55         5.26        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AN 
       65.36       133.22       134.14       125.16       108.36        96.00 
TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24Q 
       99.32        33.73       160.90        50.89       118.59       104.28 
TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 
       97.84       105.30        50.96        99.62        71.05        93.83 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB 
       39.39        33.30        10.59        77.62       275.87       129.57 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       233.62        18.77        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU 
      140.88       255.68       212.25        81.17       100.70       282.90 
TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A400 
       79.46        21.01       113.79        43.59        73.51         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AW 
       85.35        74.99        68.12        18.84       103.63        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG 
       81.44        39.55        70.22        37.22        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV 
       21.70        74.89        75.48        76.60        77.75        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 
       41.75        46.39        90.97        70.88         4.41         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY 
       81.83        24.49        23.08        20.38        12.89        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T 
        5.59        23.93        23.05        32.91        55.63         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 
       51.39        51.16        42.28        12.00        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       25.08        33.17        55.50        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A135 
       18.64        23.51        11.93        11.77        12.56        12.92 
TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 
       12.49         0.16        12.03        12.33        12.95         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 
        9.76        14.43        13.02        56.81        20.88        13.97 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK 
       19.20        16.50        18.90        12.03        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       19.40        27.58        15.22        14.73        21.83        14.50 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1Y3 TCGA-D8-A27F 
       55.30        15.85        12.99        43.04        14.14        16.04 
TCGA-D8-A27H TCGA-D8-A27T TCGA-D8-A73U TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       13.05        13.08        16.18        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A159 
       38.24        38.60        18.51        63.62        19.43        25.05 
TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II 
       12.92        76.57        53.62        37.25        33.73        33.70 
TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
       60.36       106.75       102.61        34.92        38.76        17.69 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH 
       22.29        34.16        39.55        41.62        35.24        18.94 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A22E 
        9.86         2.56        48.23        45.01        32.09        41.72 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 
       40.73         0.69         1.94         7.13        38.07        30.44 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV 
       23.84        26.70         0.79        39.72        18.90        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC 
       22.82        29.85        40.41        23.11         7.86         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-EW-A6SD 
       13.94        10.52        55.00        17.49        24.99        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
        7.40       109.87        79.10        70.85        72.10        85.15 
TCGA-GM-A2DL TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 
      115.69        69.30         2.60        11.84        11.57        32.75 
TCGA-LL-A5YM TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW 
       15.32        16.08         7.46        19.59        58.52        36.36 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX 
       20.38        23.47        41.92        28.21        86.96         0.16 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-WT-AB44 
        9.93        21.07        19.27        17.39        17.03        29.03 

$`4P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E 
       23.80        11.28        11.97        11.05        29.03        19.99 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
       33.01        33.01        17.95        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AO-A0JI TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A2LL 
       14.53        50.24         2.56        32.91        19.20        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       57.27        73.35        81.63        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A2P5 
       89.16         9.70        21.14        50.79        16.47        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G 
       29.23        25.05        14.50        40.08        18.87        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
       52.96       108.07        47.61        11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
        7.96        18.21       143.15        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP 
       87.25       101.98        55.43       136.73       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25         5.19        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       118.45 
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-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-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       18.90        32.55        25.28        50.47        21.90        49.48 
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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D 
       22.45        20.25        16.47        52.47        42.44        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
      105.34        10.59        36.23        39.65        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 
       56.28        47.31        35.93        50.83        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       26.96        21.14        21.90        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       33.11        29.79        29.56        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       10.29        13.41        14.70        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06Z 
       17.92        10.72        13.02        13.02        17.98         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98         9.01        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05        10.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       45.07        18.05        13.02         0.99        28.96        19.96 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       37.05        31.00        31.00       112.08        40.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       12.00         9.99         9.99        12.00        50.04        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-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       17.03        38.04        73.91         5.72        22.26        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        33.04        14.66        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       29.26        14.96        18.67        12.26         1.68         8.22 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C 
       20.19         1.32         2.30         0.33         0.33         1.78 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        7.36         7.46         5.65         7.59         7.17         6.90 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A03L 
        0.33         0.33         5.36         0.33         5.33        80.28 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        81.63        95.70        68.75        69.83        58.95 
TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       44.42        26.04        37.48        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       50.70        50.86        72.00        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E 
       55.33       113.62       108.72       106.78        98.27        70.42 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       53.88        40.57        20.45        97.08        82.62        24.79 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       15.62        32.52        98.33        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ 
       98.93        64.83       107.24        83.87       107.21       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
      103.86        97.68        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       61.28        86.53        86.43        94.22       120.33        99.78 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
        2.76       112.77       105.27       102.84        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       89.00        93.30        85.64       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QP TCGA-B6-A0I2 
       54.21        63.62        38.17        40.54        38.96       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IP 
      281.29        11.90        50.70        65.52       127.33       129.07 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
       68.45       234.28        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      140.28        89.46       169.51        97.48       188.68        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A40C TCGA-BH-A0AU 
      101.52       139.17       170.17        37.87        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 
       59.84        25.55        63.09        39.16        84.13        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        72.23        74.14        85.87 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       77.95        74.14        89.06        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        2.56        79.00        67.86        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        31.00        63.32        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       63.39        53.26        24.56        41.00        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        51.32        27.25 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        44.81         4.90        35.93        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-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW 
       66.05        69.93        91.99       113.82        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       49.58        17.69        31.53       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       53.98        28.14        26.14        83.31        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 
       20.12        10.52       110.60        20.88         9.63         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE 
       12.16        13.51        12.59        12.59        12.46        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       10.92        11.34        11.28        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A 
       12.53        12.36        15.45        16.87        16.70        24.56 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 
       33.99        12.95        12.49        13.41        19.46        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB 
       20.58        14.17        13.48        14.17        17.49        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.15        53.00        14.01        18.97        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-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT 
       17.16        19.92        17.69        16.41        16.31        16.64 
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-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       17.06         1.61        10.09        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       18.51        21.67        12.66        25.22        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-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       28.87        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       31.96        69.34        69.96        23.24        21.04        23.87 
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-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        14.07        51.39        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       28.50        77.65        37.41        70.36        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
        3.88        22.19        60.99        11.08        54.18        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       24.59        75.81        28.90         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       43.56         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        36.20        36.56        35.77        25.84        24.82 
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        11.15        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       41.03        40.50        20.12        38.99        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO 
       29.72         9.47        32.91        30.18        23.90        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       26.40        27.85        12.20         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       16.57        28.77        29.95        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PG 
       18.48        30.08        18.90        19.99        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       19.96        52.73        25.91        22.09        34.03        17.52 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        15.22        16.77        31.30        59.57       216.76 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       83.34        86.96       106.06       101.62       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        62.47 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YN 
       21.24         7.10        13.28        10.62        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        22.26         2.63        15.68        19.53        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       58.62        34.92        28.87        24.72        22.32        26.70 
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-PL-A8LY TCGA-S3-A6ZF 
       40.11         8.91        47.01        64.21         0.26        18.81 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ 
       18.48        20.68        13.84        17.26         3.81        66.84 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           282.90            281.29 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            25.48             28.90 
[1] "0.0 - 282.9 (25.5)" "0.3 - 281.3 (28.9)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        27       17        0        1       121        87
  4P LOSS WILD-TYPE      62       66        6        5       231       166
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  4P LOSS MUTATED           0         54         10         21        7       4
  4P LOSS WILD-TYPE         2        101         17         44       13       9
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 27                62
  STAGE IA                17                66
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA              121               231
  STAGE IIB               87               166
  STAGE III                0                 2
  STAGE IIIA              54               101
  STAGE IIIB              10                17
  STAGE IIIC              21                44
  STAGE IV                 7                13
  STAGE X                  4                 9
[1] 12  2
[1] TRUE
[1] "dimension of 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    71 226  39  15
  4P LOSS WILD-TYPE 203 399  98  25
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              71               203
  T2             226               399
  T3              39                98
  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   163 116  46  23
  4P LOSS WILD-TYPE 343 242  73  54
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             163               343
  N1             116               242
  N2              46                73
  N3              23                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"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   298   7
  4P LOSS WILD-TYPE 591  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    298    7
  4P LOSS WILD-TYPE  591   15
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             298               591
  1               7                15
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   349   4
  4P LOSS WILD-TYPE 718   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    349    4
  4P LOSS WILD-TYPE  718    8
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE             349               718
  MALE                 4                 8
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   140 177
  4P LOSS WILD-TYPE 297 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    140  177
  4P LOSS WILD-TYPE  297  370
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              140               297
  YES             177               370
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P LOSS MUTATED                            1                           291
  4P LOSS WILD-TYPE                          0                           477
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P LOSS MUTATED                               34                   3
  4P LOSS WILD-TYPE                            167                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P LOSS MUTATED                       4                                6
  4P LOSS WILD-TYPE                     5                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  4P LOSS MUTATED                    0             13
  4P LOSS WILD-TYPE                 17             33
D48V9, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                291               477
  INFILTRATING LOBULAR CARCINOMA                34               167
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                13                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"
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                          79   228
  4P LOSS WILD-TYPE                       102   516
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                     79               102
  WHITE                                        228               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"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 291
  4P LOSS WILD-TYPE  28 583
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  291
  4P LOSS WILD-TYPE   28  583
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             291               583
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   259  47
  4Q LOSS WILD-TYPE 658 101
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              306               759 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               47               101 
$`4Q LOSS MUTATED`
TCGA-A7-A26I TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A09C 
       21.73        53.06        19.99        15.06        33.01         1.02 
TCGA-A8-A09E TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AR-A1AM 
       49.05        19.33        13.71        17.79         5.65        98.33 
TCGA-C8-A1HL TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-S3-AA17 TCGA-3C-AAAU TCGA-3C-AALJ 
       10.42        73.64        50.07        13.94       133.05        48.46 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
       20.88        31.79        39.32        28.01        18.02       101.98 
TCGA-A2-A0CL TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ 
       99.12        77.19        98.99       107.93        67.33        79.76 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ 
       27.12        50.43        17.13        20.75        18.21        18.61 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4RX 
       17.36        19.20        17.19        91.07        50.37        24.39 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G 
       35.31        30.61        35.67        31.73        25.15        23.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW 
       14.50        21.17        17.92        14.73        10.29         9.37 
TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       10.42         1.02        31.00        26.01         1.02        17.03 
TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R 
       43.00         8.98        38.01        12.00         9.99         0.99 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK 
       43.00        30.97         8.98        14.01        22.95        73.05 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y 
       19.33        32.45         6.48        16.80        11.44        17.42 
TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
       13.58         0.03         1.12         0.23         0.33         0.62 
TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        9.96         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP 
        7.00         0.33         0.36         0.33         0.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.33         0.33         5.59        66.77        32.78        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 
       20.32        72.00        76.77        71.80       115.27       108.03 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04L 
      102.31        82.68        60.56        61.87        11.51       130.09 
TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH 
        5.26        55.86        65.36       133.22       134.14       125.16 
TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O 
       96.00        99.32        33.73       160.90        50.89       118.59 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A256 
      104.28        97.84       105.30        50.96        99.62        93.83 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ 
       10.59        77.62       275.87       129.57       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH 
       18.77        84.59       165.76       140.88       255.68       212.25 
TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC 
       81.17       282.90        79.46        21.01       113.79        43.59 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW 
       73.51        85.35        68.12       103.63        59.84        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ 
       81.44        39.55        70.22        37.22        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 
       74.89        75.48        76.60        77.75        49.94        41.75 
TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GZ 
       46.39         4.41         9.63        81.83        24.49        10.78 
TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       23.08        20.38        12.89        50.79         5.59        23.93 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       23.05        32.91        55.63        51.39        51.16        69.93 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU 
       42.28        12.00        97.48        25.08        33.17        55.50 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L 
       38.60        57.83       130.16        18.64        23.51        11.93 
TCGA-C8-A12P TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26Y 
       11.77        12.49         0.16        12.03        12.33        12.95 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z 
        9.76        14.43        13.02        13.41        56.81        20.88 
TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       16.50        18.90        12.03        20.09        20.12        19.40 
TCGA-D8-A1JP TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR 
       21.01        14.73        21.83        14.50        55.30        15.85 
TCGA-D8-A1XU TCGA-D8-A27H TCGA-D8-A27T TCGA-D8-A73U TCGA-E2-A14N TCGA-E2-A14O 
       12.99        13.05        13.08        16.18        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15H 
       38.24        38.60        63.62        19.43        25.05        12.92 
TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L7 
       14.07        53.62        37.25        33.73        33.70        60.36 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 
      106.75       102.61        34.92        38.76        17.69        22.29 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1NI 
       34.16        39.55        41.62        35.24        18.94         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E 
        2.56         6.12        45.01        32.09        34.45        41.72 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 
       40.73         0.69         1.94         7.13        38.07        30.44 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV 
       23.84        26.70         0.79        39.72        18.90        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC 
       22.82        29.85        40.41        23.11         7.86         6.15 
TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SB 
       10.52        19.96        55.00        17.49        16.77        24.99 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A3XL 
       33.21         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        32.75        15.32        16.08 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
        7.46        19.59        58.52        36.36        20.38        41.92 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-WT-AB44 
       86.96         0.16        21.07        17.39        17.03        29.03 

$`4Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        22.32        11.28        11.97        11.05        29.03 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01        33.01        17.95        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AO-A0JI TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       19.79        14.53        50.24         2.56        32.91        19.20 
TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       17.23        66.15        57.27        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 
       32.58        21.44        89.16         9.70        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       50.79        16.47        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       14.50        40.08        18.87        11.41        52.96       108.07 
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
      131.67        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM 
       43.43        48.10        14.27        47.24        13.68         7.96 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        24.79       114.81        92.48       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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       20.25        16.47        52.47        42.44        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       56.28        47.31        35.93        50.83         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        26.96        21.14        21.90        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26J 
       37.45        33.11        29.79        20.19        29.56        20.61 
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-A4SB TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       13.74        12.10        10.72         8.75        13.02        13.02 
TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       17.98        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-A08T 
       28.96        19.96        37.05        31.00        31.00       112.08 
TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       50.04        33.07         1.02        25.02        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-A23H 
       27.02        17.03        38.04        19.23        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       22.26        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN 
       87.12        26.04        74.14        33.04        14.66        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IX 
       23.24        24.79        29.26        14.96        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         8.22        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         2.96         1.78         1.71         7.36         7.46 
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         6.90         7.04 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XU 
        0.33         0.33         5.36        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 
       69.83        58.95        44.42        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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       26.24        62.04        55.33       113.62       108.72       106.78 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        70.42        53.88        40.57        20.45        97.08 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       82.62        24.79        26.93        15.62        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       98.33        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      107.24        83.87       107.21       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       97.68        86.07        93.90        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P 
       86.53        86.43        94.22       120.33        99.78         2.76 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      112.77       105.27       102.84        98.76        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE 
       38.96       143.38       281.29        11.90        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
      146.50       127.33       129.07        68.45       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 
      169.51        97.48       188.68        18.35       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      245.10        28.27        68.94        58.55       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40C 
      170.17        37.87         7.07        74.99        18.84        71.15 
TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 
       62.93        25.55        63.09        39.16        84.13        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       32.02        18.21        61.51        61.68        72.23        74.14 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       85.87        77.95        74.14        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI 
       16.27        15.68        14.30        44.81        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       30.35        15.16        63.39        53.26        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         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EO TCGA-BH-A1ES 
       30.28        37.55        66.05         7.36        91.99       113.82 
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-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62       114.15        74.73       122.83        33.99        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        53.98        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       20.88         9.63         5.26        18.87        21.76         9.44 
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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56        12.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.59        12.92        12.46        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.28        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A 
       12.36        15.45        16.87        16.70         0.03        24.56 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 
       33.99        12.95        12.49        19.46        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        19.20        14.17        17.49 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        18.15        53.00        14.01        18.97 
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-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-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       12.39        17.16        15.22        19.92        17.69        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31        16.64        15.16        43.04        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-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        14.43        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        10.09        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       21.67        12.66        25.22        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-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       40.96        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 
       31.96        69.34        18.51        69.96        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       23.87        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        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        51.39        76.57        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       32.35        28.50        77.65        37.41        70.36        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL 
       19.66        24.59        75.81        28.90         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 
       34.55        43.56         8.28        30.61        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG 
       32.88        36.82        36.20        36.56        35.77        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       24.82        28.27        34.95         3.02        11.15        48.23 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       47.64        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       41.03        40.50        20.12        38.99        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO 
       29.72         9.47        32.91        30.18        23.90        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       26.40        27.85        12.20         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       16.57        28.77        29.95        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF 
       18.48        30.08        18.90        19.99        13.94        14.43 
TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       34.55        52.73        25.91        22.09        34.03        17.52 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        15.22        31.30       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       79.10        83.34        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-A2OB TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       18.12        62.47        21.24         7.10        13.28        10.62 
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-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       19.53        12.36        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        23.47        65.62        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-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       47.01        64.21         0.26         9.93        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ 
       20.68        19.27        13.84        17.26         3.81        66.84 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.03              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           282.90            281.29 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           25.975            28.440 
[1] "0.0 - 282.9 (26.0)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        22       18        0        2       104        75
  4Q LOSS WILD-TYPE      67       65        6        4       248       178
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  4Q LOSS MUTATED           0         48          9         18        7       5
  4Q LOSS WILD-TYPE         2        107         18         47       13       8
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 22                67
  STAGE IA                18                65
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA              104               248
  STAGE IIB               75               178
  STAGE III                0                 2
  STAGE IIIA              48               107
  STAGE IIIB               9                18
  STAGE IIIC              18                47
  STAGE IV                 7                13
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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    61 193  40  15
  4Q LOSS WILD-TYPE 213 432  97  25
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              61               213
  T2             193               432
  T3              40                97
  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   143 103  38  21
  4Q LOSS WILD-TYPE 363 255  81  56
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             143               363
  N1             103               255
  N2              38                81
  N3              21                56
[1] 4 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   261   7
  4Q LOSS WILD-TYPE 628  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    261    7
  4Q LOSS WILD-TYPE  628   15
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             261               628
  1               7                15
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   308   3
  4Q LOSS WILD-TYPE 759   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    308    3
  4Q LOSS WILD-TYPE  759    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE             308               759
  MALE                 3                 9
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   122 157
  4Q LOSS WILD-TYPE 315 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    122  157
  4Q LOSS WILD-TYPE  315  390
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              122               315
  YES             157               390
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q LOSS MUTATED                            0                           253
  4Q LOSS WILD-TYPE                          1                           515
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q LOSS MUTATED                               32                   2
  4Q LOSS WILD-TYPE                            169                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q LOSS MUTATED                       4                                6
  4Q LOSS WILD-TYPE                     5                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  4Q LOSS MUTATED                    0             13
  4Q LOSS WILD-TYPE                 17             33
D49V9, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                253               515
  INFILTRATING LOBULAR CARCINOMA                32               169
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                13                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"
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                          68   198
  4Q LOSS WILD-TYPE                       113   546
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                     68               113
  WHITE                                        198               546
[1] 4 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    10 248
  4Q LOSS WILD-TYPE  29 626
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10  248
  4Q LOSS WILD-TYPE   29  626
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                29
  NOT HISPANIC OR LATINO             248               626
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED   114  25
  5P LOSS WILD-TYPE 803 123
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              139               926 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               123 
$`5P LOSS MUTATED`
TCGA-A7-A26I TCGA-A8-A06T TCGA-A8-A084 TCGA-AR-A1AR TCGA-GM-A2DD TCGA-WT-AB41 
       21.73        53.06        15.06        17.23        75.02        52.96 
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-A0T1 TCGA-A2-A0YH 
       24.79        67.33        63.29        50.43        17.13        21.67 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX 
       18.61        31.73        19.20        33.93        91.07        47.31 
TCGA-A2-A3XY TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A4SE TCGA-A7-A6VY TCGA-A8-A075 
       35.93        35.67        20.19        21.17         8.75        17.03 
TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A08X TCGA-AC-A2BK TCGA-AC-A6IW 
       53.98         9.99         8.98        43.00        73.05        13.58 
TCGA-AN-A041 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FL 
        0.23         7.36         7.46         0.33         0.33         7.59 
TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A124 
        7.04         0.33        52.18        26.04        50.70       115.27 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0U0 TCGA-AR-A0U2 
      108.03        60.56        26.93       130.09        65.36        83.87 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S 
      125.16       101.00        99.32        50.89       104.28        97.84 
TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IO 
       89.00        99.62       129.57        65.52       146.50       165.76 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A402 TCGA-BH-A0B4 TCGA-BH-A0BG 
      102.77       100.70       282.90        74.99        39.16        61.51 
TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0WA TCGA-BH-A18T 
       77.75        41.75         4.41        52.96        23.05         7.36 
TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A209 
       51.16       114.15        74.73        72.07        55.50       130.16 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A26W 
       11.93        12.66        12.59        12.49        10.92        12.53 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A9FZ TCGA-D8-A147 TCGA-D8-A1JB 
       12.36         9.76        24.56        19.46        19.20        55.50 
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        76.57 
TCGA-E2-A1B6 TCGA-E2-A1L7 TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 
       28.50        60.36       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 
       34.16        39.55        41.62        35.24        41.03        40.73 
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-EW-A6S9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       25.91        15.22        70.85        69.30         2.60        11.84 
TCGA-LL-A441 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A6VO 
       32.75        58.52        36.36        23.47        65.62        28.21 
TCGA-S3-AA10 
       19.27 

$`5P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        22.32        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       19.99        33.01        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI 
       49.05        45.07        29.98        16.57        19.79        14.53 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       19.33        13.71        50.24        17.79         5.65         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       32.91        19.20        98.33        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U 
       50.07        26.99        15.68        52.96        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       24.95        29.23        25.05        14.79        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI 
       18.87        13.94        11.41       108.07       133.05       131.67 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       48.46        47.61        11.44         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04W 
       39.32        18.21       143.15        78.41       121.94       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        99.12       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       77.19        75.25         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-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       118.45        79.76        74.40        72.00        35.05 
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-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-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       18.21        50.47        21.90        49.48        19.33        48.46 
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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        36.23        39.65        29.98        32.75        56.28 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         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-A0DC TCGA-A7-A13D TCGA-A7-A13F 
       30.61        37.45        33.11        29.79        31.73        25.15 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       13.41        14.70        14.93        13.74        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        10.29         9.37        10.42 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        1.02         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05        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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 
       31.00         0.99       112.08        40.01        30.97        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       12.00         9.99         9.99        12.00        50.04        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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       29.26        16.80        14.96        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-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        2.96         1.78         1.71         9.96         0.16         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         6.90 
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         5.36         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-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        69.83        58.95        44.42        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-A0JJ 
       50.86        72.00        76.77        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       55.33        71.80       113.62       108.72       106.78       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A1H2 
       97.08        61.87        82.62        11.51        24.79        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86       107.24       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      134.14       107.21       108.36       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        93.90        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      118.59         2.76       112.77       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       50.96        98.76        98.66        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       281.29        11.90       275.87        50.70 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       233.62        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       140.28        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        85.35        68.12        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.55        70.22        84.13        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        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       74.14        46.39        89.06        90.97        81.73        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       67.10        38.01        29.98        13.91        78.28        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        79.00        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        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        32.91         4.90        35.93        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-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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG 
       31.53        97.48        25.08       120.62        33.17       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       33.99        63.35        55.00        45.63        53.98        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31        57.83        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        9.63         5.26        18.87        21.76         9.44        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56        12.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92        12.46        12.33        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y 
       12.03        12.33        12.95        12.33        20.25        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 
       15.45        16.87        16.70         0.03        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95        13.02        12.49        13.41        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 
       13.25        20.58        13.97        14.17        13.48        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        53.00 
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        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
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        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       17.06         1.61        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        12.66        25.22        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        75.98        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 
       69.34        18.51        63.62        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       21.04        23.87        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        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       11.05        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       87.22        33.01        32.35        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.19        60.99        11.08        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       75.81        28.90       106.75        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        22.29        36.20        36.56        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        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        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       38.37        41.72        40.50        20.12        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        28.77        25.94 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.95        40.41        39.78        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08        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-A2FW 
       14.43        34.55        19.96        55.00        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        17.52        23.51        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        83.34        72.10        85.15        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-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        62.47        11.57        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        7.10        13.28        10.62        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX 
        2.10        36.30        31.99        58.62        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L 
       24.72        22.32        20.38        26.70        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-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 
       18.81        18.48        21.07        20.68        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.23              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           282.90            281.29 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            33.93             27.07 
[1] "0.2 - 282.9 (33.9)" "0.0 - 281.3 (27.1)"
[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        58        32
  5P LOSS WILD-TYPE      80       76        6        6       294       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  5P LOSS MUTATED           0         20          2         10        2       0
  5P LOSS WILD-TYPE         2        135         25         55       18      13
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 7                76
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               58               294
  STAGE IIB               32               221
  STAGE III                0                 2
  STAGE IIIA              20               135
  STAGE IIIB               2                25
  STAGE IIIC              10                55
  STAGE IV                 2                18
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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    28  98  11   5
  5P LOSS WILD-TYPE 246 527 126  35
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              28               246
  T2              98               527
  T3              11               126
  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    69  45  16  11
  5P LOSS WILD-TYPE 437 313 103  66
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              69               437
  N1              45               313
  N2              16               103
  N3              11                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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   119   2
  5P LOSS WILD-TYPE 770  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    119    2
  5P LOSS WILD-TYPE  770   20
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0             119               770
  1               2                20
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   141   1
  5P LOSS WILD-TYPE 926  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    141    1
  5P LOSS WILD-TYPE  926   11
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE             141               926
  MALE                 1                11
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    59  70
  5P LOSS WILD-TYPE 378 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     59   70
  5P LOSS WILD-TYPE  378  477
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               59               378
  YES              70               477
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P LOSS MUTATED                            0                           121
  5P LOSS WILD-TYPE                          1                           647
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P LOSS MUTATED                                3                   4
  5P LOSS WILD-TYPE                            198                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P LOSS MUTATED                       0                                5
  5P LOSS WILD-TYPE                     9                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  5P LOSS MUTATED                    0              8
  5P LOSS WILD-TYPE                 17             38
D50V9, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                121               647
  INFILTRATING LOBULAR CARCINOMA                 3               198
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                25
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 8                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"
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  1    12
  5P LOSS WILD-TYPE                                0    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          32    88
  5P LOSS WILD-TYPE                       149   656
D50V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         12                48
  BLACK OR AFRICAN AMERICAN                     32               149
  WHITE                                         88               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"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3 120
  5P LOSS WILD-TYPE  36 754
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3  120
  5P LOSS WILD-TYPE   36  754
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             120               754
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   191  33
  5Q LOSS WILD-TYPE 726 115
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              224               841 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               115 
$`5Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26I TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A09K TCGA-AC-A62X 
       19.20        21.73        15.06        33.01        29.98        13.71 
TCGA-AQ-A54N TCGA-AR-A1AR TCGA-E2-A158 TCGA-GM-A2DD TCGA-LL-A5YP TCGA-WT-AB41 
        2.56        17.23        14.79        75.02        14.79        52.96 
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q 
      131.67         9.96        31.79        28.01        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 
       73.84        87.25       101.98        24.79        67.33        34.55 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0YH TCGA-A2-A0YJ 
       79.76        63.29        50.43        17.13        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        91.07        47.31        35.93 
TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G 
        7.30        21.90        35.67        31.73        20.19        23.74 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VY 
       21.17        17.92        14.73        12.10        10.29         8.75 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
       31.00        17.03        53.98         9.99         8.98        24.99 
TCGA-A8-A08X TCGA-A8-A09A TCGA-AC-A2BK TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A8OQ 
       43.00         9.99        73.05        14.96        13.58         1.12 
TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        0.23         1.78         7.36         7.46         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.96         7.59         7.04         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A0JL 
        0.33         0.33        52.18        26.04        50.70        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L 
      115.27       108.03        60.56        82.62        26.93       130.09 
TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ 
      140.55       109.02        65.36        83.87       125.16       101.00 
TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U 
       99.32        33.73        50.89       104.28        97.84       102.84 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG 
       98.66        89.00        99.62       129.57        65.52       146.50 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX 
      165.76       255.68       102.77       100.70       282.90        21.01 
TCGA-B6-A1KF TCGA-B6-A3ZX TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BF 
      101.52        37.87        74.99        59.84        39.55        43.53 
TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 
       61.51        75.48        77.75        77.95        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        55.50        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        12.16        13.51 
TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W 
       12.59        12.49        10.92         0.16        12.33        12.53 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A8HR TCGA-C8-A9FZ 
       12.36         9.76        24.56        14.43        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        55.50        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        16.64        43.04 
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-A159 TCGA-E2-A15A 
       40.11        47.15        63.62        21.04        25.05        23.34 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 
       76.57        53.62        28.50        33.70        60.99        60.36 
TCGA-E2-A1LA TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 
       24.59       102.61         8.75        43.04        34.92        38.76 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22D 
       34.16        39.55        41.62        32.09        46.59        41.03 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P4 
       40.73         0.69        30.18        22.82        41.13        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A6S9 TCGA-EW-A6SA 
        7.86        18.90        19.96        25.91        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL 
       24.99        33.21       109.87        70.85        72.10        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FR 
        2.60        11.84        32.75        15.32        14.70        16.08 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J 
       58.52        36.36        22.32        20.38        23.47        65.62 
TCGA-PL-A8LX TCGA-S3-AA10 
        0.16        19.27 

$`5Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
      107.70        38.30        23.61        31.36        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       19.99        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI 
       45.07        16.57        19.79        14.53        19.33        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL 
       17.79         5.65        32.91        19.20        98.33        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       57.27        73.35        81.63        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC 
       89.16         9.70        10.42        21.14        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO 
       73.64        50.07        26.99        15.68        52.96        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU 
       13.22        24.95        29.23        25.05        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALJ 
       18.87        13.94        11.41       108.07       133.05        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       47.61        11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
       18.21       143.15       121.94        55.43       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        56.81        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       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       35.05        34.29        31.82        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 
       54.64        27.12        44.88        44.28        17.52         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-A0YI TCGA-A2-A0YK 
       25.28        18.21        50.47        21.90        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-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       20.25        16.47        52.47        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
      105.34        10.59        36.23        39.65        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       56.28        50.37        50.83        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.14        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J 
       37.45        33.11        29.79        25.15        29.56        20.61 
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-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       13.74        14.50        10.72         9.37        10.42        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 
       13.02         1.02        17.98        26.01         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 
       10.98         7.99         9.99        45.07        18.05        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-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       40.01        30.97        41.98        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       50.04        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        19.23 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
       22.95        73.91         5.72        22.26        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       33.04        19.33        14.66        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62Y 
       23.24        24.79        29.26        16.80        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         6.90         0.36         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        5.36        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        69.83        58.95        44.42        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-A0JJ 
       50.86        72.00        76.77        65.10        26.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       71.80       113.62       108.72       106.78       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       82.68        70.42        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ 
       61.87        11.51        24.79        15.62        32.52        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        84.10        75.22        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       133.22       134.14       107.21       108.36       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.53        86.43       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V 
       99.78       118.59         2.76       112.77       105.27       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       50.96        98.76        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IH 
      143.38       281.29        11.90       275.87        50.70       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      233.62        18.77       127.33        84.59       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       140.28        89.46       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.46        18.35       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        68.94        58.55        43.59        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
      170.17         7.07        85.35        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        21.70        74.89        61.68        72.23        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       76.60        85.87        49.94        74.14        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       67.86        70.88        16.27        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       81.83        24.49        31.00        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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-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        32.91         4.90        35.93 
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-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        69.93        91.99 
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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG 
       25.81        97.48        25.08       120.62        33.17       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       33.99        63.35        55.00        45.63        53.98        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       110.60        20.88        23.51         9.63         5.26 
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-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG 
       12.56        12.59        12.92        12.46        12.33        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y 
       11.28        12.03        12.95        12.33        20.25        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 
       15.45        16.87        16.70         0.03        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.02        12.49        56.81        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       14.17        13.48        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        53.00        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 
       55.30        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 
       48.03        16.41        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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        75.98        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        69.34        18.51        69.96        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        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        14.07        51.39        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       32.35        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        22.19        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A2P6 TCGA-E2-A3DX 
       19.66        75.81        28.90       106.75        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF 
       36.82        22.29        36.20        36.56        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        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        11.15        48.23        45.01 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        21.27        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       41.72        40.50        20.12        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.90        13.25        16.57        28.77        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.85        40.41        39.78        23.11        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-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        17.52 
TCGA-EW-A424 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       23.51        31.30         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-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-A7W5 TCGA-LD-A7W6 
       18.12        62.47        11.57        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       10.62        17.06        14.47        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        19.53        12.36        19.59        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
       22.39         2.10        36.30        31.99        58.62        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        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       18.48        21.07        20.68        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.16              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           282.90            281.29 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            27.47             28.27 
[1] "0.2 - 282.9 (27.5)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       11        0        2        93        54
  5Q LOSS WILD-TYPE      73       72        6        4       259       199
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  5Q LOSS MUTATED           0         27          4         12        5       2
  5Q LOSS WILD-TYPE         2        128         23         53       15      11
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 16                73
  STAGE IA                11                72
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               93               259
  STAGE IIB               54               199
  STAGE III                0                 2
  STAGE IIIA              27               128
  STAGE IIIB               4                23
  STAGE IIIC              12                53
  STAGE IV                 5                15
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    45 155  19   8
  5Q LOSS WILD-TYPE 229 470 118  32
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              45               229
  T2             155               470
  T3              19               118
  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   117  71  24  13
  5Q LOSS WILD-TYPE 389 287  95  64
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             117               389
  N1              71               287
  N2              24                95
  N3              13                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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   195   5
  5Q LOSS WILD-TYPE 694  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    195    5
  5Q LOSS WILD-TYPE  694   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             195               694
  1               5                17
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   227   1
  5Q LOSS WILD-TYPE 840  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    227    1
  5Q LOSS WILD-TYPE  840   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE             227               840
  MALE                 1                11
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    94 112
  5Q LOSS WILD-TYPE 343 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     94  112
  5Q LOSS WILD-TYPE  343  435
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               94               343
  YES             112               435
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q LOSS MUTATED                            1                           201
  5Q LOSS WILD-TYPE                          0                           567
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q LOSS MUTATED                                5                   5
  5Q LOSS WILD-TYPE                            196                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q LOSS MUTATED                       0                                5
  5Q LOSS WILD-TYPE                     9                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  5Q LOSS MUTATED                    0             10
  5Q LOSS WILD-TYPE                 17             36
D51V9, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                201               567
  INFILTRATING LOBULAR CARCINOMA                 5               196
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                25
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                10                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"
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1    18
  5Q LOSS WILD-TYPE                                0    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          63   130
  5Q LOSS WILD-TYPE                       118   614
D51V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     63               118
  WHITE                                        130               614
[1] 4 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     7 190
  5Q LOSS WILD-TYPE  32 684
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7  190
  5Q LOSS WILD-TYPE   32  684
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             190               684
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   164  24
  6P LOSS WILD-TYPE 753 124
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              188               877 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               124 
$`6P LOSS MUTATED`
TCGA-A1-A0SP TCGA-A2-A0CQ TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A09C 
       19.20        88.60        22.32        53.06        33.01         1.02 
TCGA-A8-A09K TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-BH-A1F5 TCGA-E2-A1L8 
       29.98        17.79         2.56        32.91        89.16        73.64 
TCGA-GM-A2DD TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W 
       75.02       133.05        48.46       121.94        87.25       101.98 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D4 
      107.93        77.19        75.25         5.19        98.99        25.22 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A1FV 
       80.28        27.12        49.84        20.52        20.75        23.47 
TCGA-A2-A1FW TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A8-A06O 
       17.36        39.65        56.28        21.30        31.73        13.02 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08G 
       26.01         1.02         9.01        12.00         7.99        19.96 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       12.00        31.00        12.00        33.07         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G 
       19.04        13.02        21.04        27.02        17.03        73.91 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62Y 
       99.35        26.04        32.45        29.26        16.80        17.42 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A04C TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX 
       20.19         1.32         1.78         5.65         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03T TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG 
        5.59        69.83        37.48        20.32        22.36        26.24 
TCGA-AO-A0JJ TCGA-AO-A1KR TCGA-AR-A0TQ TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A24K 
       62.04        82.62        98.33        93.90        94.29        50.89 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 TCGA-AR-A256 TCGA-B6-A0IA 
        2.76       112.77       105.30        93.30        93.83       275.87 
TCGA-B6-A0IJ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B0 
      233.62       162.05        79.46        85.35        62.93        81.44 
TCGA-BH-A0B5 TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0DP 
       70.22        75.48        41.75        89.06        78.28        15.65 
TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX 
       14.30        63.32        23.08        26.50        51.32        27.25 
TCGA-BH-A0W3 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1EU 
       23.93        35.93        26.66        66.05       113.82        42.28 
TCGA-BH-A1EY TCGA-BH-A1FE TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A42V TCGA-BH-A5J0 
       17.69        74.73        63.35        45.63        20.88        23.51 
TCGA-BH-A8FZ TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG 
       18.87        12.66        11.77        12.66        12.46        11.34 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A145 
       16.70        24.56        13.02        13.41        19.46        13.48 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF 
       15.78        18.90        53.00        19.40        27.58        15.22 
TCGA-D8-A1XU TCGA-D8-A1Y1 TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 
       12.99         9.93        12.26        12.66        34.42        46.59 
TCGA-E2-A10C TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F 
       40.11        34.26        69.96        23.24        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1LE 
       12.92        56.94        76.57        37.25        77.65        28.90 
TCGA-E2-A1LL TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE 
       43.04        17.69        22.29        34.16        36.56        35.77 
TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG 
       35.24        24.82        11.15        45.01        32.09        21.27 
TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS 
       47.64        37.74        39.09         1.94         7.13        29.72 
TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A6S9 
       30.44        26.40        18.90        28.77        23.11        15.22 
TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A7SZ 
       33.21        79.10        83.34        69.30        15.32        19.53 
TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-S3-A6ZG 
       19.59        22.39        28.21        19.73        40.11        18.48 
TCGA-S3-AA14 TCGA-UU-A93S 
       17.39         3.81 

$`6P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A2-A25A 
       48.56        48.36        63.12        36.13        19.56       107.70 
TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
       38.30        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        11.05        29.03        19.99        15.06 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A3W5 
       33.01        33.01        17.95        49.05        45.07        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AQ-A0Y5 
       19.79        14.53        19.33        13.71        50.24         5.65 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       19.20        98.33        17.23        66.15        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A8FY TCGA-C8-A1HL 
       81.63        54.05        32.58        21.44         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1LG TCGA-E2-A2P5 
       21.14        14.79        50.79        16.47        50.07        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       15.68        52.96        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK 
       11.41        52.96       108.07       131.67        47.61        11.44 
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-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       28.01        18.21       143.15        18.02        78.41        73.84 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
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-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40       118.45        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-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-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.13         8.38        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-A0YM TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        31.73        23.77        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       20.25        19.20        16.47        52.47        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15       105.34        10.59        36.23        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        23.21        26.96        21.14        21.90 
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-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G 
       33.11        29.79        20.19        25.15        29.56        23.74 
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-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-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       13.02         1.02        17.98        31.00        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O 
       43.00        18.97        18.97        14.01        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         8.98        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-A08J 
       36.95        13.02         0.99        38.01        28.96        37.05 
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-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       30.97        41.98         9.99         9.99        12.00        50.04 
TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       25.02        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        38.04        19.23        22.95         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       73.05        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        33.04        19.33        14.66         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79        14.96        11.44        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OS 
       12.26         1.68         8.22         0.03         1.12         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         7.46         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         6.44         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.90         7.04         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         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-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        95.70        68.75        58.95        44.42        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       21.40        52.18        26.04        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JL TCGA-AO-A0JM 
       50.86        72.00        76.77        65.10        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        61.87        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS 
      130.09        15.62        32.52       140.55         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        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       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       99.32        37.81        61.28        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q 
      160.90        94.22       120.33        99.78       118.59       104.28 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84       105.27       102.84        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       89.00        99.62        85.64        71.05       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       33.30        38.96        10.59        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       11.90       129.57        50.70        65.52       146.50       112.37 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       102.77       140.28       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      169.51        97.48       188.68        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        74.99        68.12        18.84       103.63        71.15 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        20.45        25.55        63.09        39.55        39.16 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       61.51        21.70        74.89        61.68        72.23        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        85.87        77.75        49.94        77.95        74.14 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       46.39        90.97        81.73        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       29.98        13.91         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       81.83        24.49        31.00        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI 
       63.39        53.26        24.56        41.00        52.96        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        32.91 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        4.90        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        25.08       120.62       114.15        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
      122.83        33.99        55.00        72.07        53.98        55.50 
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-A5IZ 
       36.82        36.79        20.12        10.52       110.60        18.64 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.63         5.26        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.56        12.16        13.51        12.59        12.59        12.92 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.49        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       12.95        15.45        16.87         0.03         9.76        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       33.99        12.95        12.49        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        14.17        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        55.50        18.15        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.12        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-A1XG TCGA-D8-A1XJ 
       23.90        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        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31        16.64        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52        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        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        10.09        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       21.67        16.18        25.22        43.00        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       37.51        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-A14W 
       38.24        38.60        33.17        75.98        43.33        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 
       31.96        69.34        18.51        63.62        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G 
       23.87        25.05        23.34        22.82        17.29        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI 
       60.36        19.66        24.59        75.81       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
        8.75        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 
       38.76        34.29        34.82        32.88        36.82        36.20 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 
       39.55        41.62        25.84        18.94         9.86        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        48.23        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
        1.12        46.65         6.58        46.59        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       42.25        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       20.12         0.69        38.99        24.56        12.33         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       38.07        32.91        30.18        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.21        13.25        16.57        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 
       29.85        40.41        41.13        39.78        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        17.52        23.51 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       16.77        24.99        31.30         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        70.85        72.10        85.15        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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        14.70        14.47        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       15.68         7.46        12.36        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        34.92        36.36 
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-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
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        18.81        21.07        20.68        19.27        13.84 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.26        17.03        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.33              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           275.87            282.90 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            27.07             28.44 
[1] "0.3 - 275.9 (27.1)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED        14       16        2        0        65        49
  6P LOSS WILD-TYPE      75       67        4        6       287       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  6P LOSS MUTATED           0         25          5          7        4       3
  6P LOSS WILD-TYPE         2        130         22         58       16      10
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                16                67
  STAGE IB                 2                 4
  STAGE II                 0                 6
  STAGE IIA               65               287
  STAGE IIB               49               204
  STAGE III                0                 2
  STAGE IIIA              25               130
  STAGE IIIB               5                22
  STAGE IIIC               7                58
  STAGE IV                 4                16
  STAGE X                  3                10
[1] 12  2
[1] TRUE
[1] "dimension of 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    53 110  19   7
  6P LOSS WILD-TYPE 221 515 118  33
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              53               221
  T2             110               515
  T3              19               118
  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 LOSS MUTATED    88  70  19  11
  6P LOSS WILD-TYPE 418 288 100  66
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              88               418
  N1              70               288
  N2              19               100
  N3              11                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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   164   4
  6P LOSS WILD-TYPE 725  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    164    4
  6P LOSS WILD-TYPE  725   18
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0             164               725
  1               4                18
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   189   1
  6P LOSS WILD-TYPE 878  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    189    1
  6P LOSS WILD-TYPE  878   11
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE             189               878
  MALE                 1                11
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    70 103
  6P LOSS WILD-TYPE 367 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     70  103
  6P LOSS WILD-TYPE  367  444
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               70               367
  YES             103               444
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P LOSS MUTATED                            0                           145
  6P LOSS WILD-TYPE                          1                           623
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P LOSS MUTATED                               26                   0
  6P LOSS WILD-TYPE                            175                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P LOSS MUTATED                       1                                7
  6P LOSS WILD-TYPE                     8                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  6P LOSS MUTATED                    5              6
  6P LOSS WILD-TYPE                 12             40
D52V9, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                145               623
  INFILTRATING LOBULAR CARCINOMA                26               175
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                23
  MUCINOUS CARCINOMA                             5                12
  OTHER, SPECIFY                                 6                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"
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                          33   120
  6P LOSS WILD-TYPE                       148   624
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                     33               148
  WHITE                                        120               624
[1] 4 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     5 149
  6P LOSS WILD-TYPE  34 725
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5  149
  6P LOSS WILD-TYPE   34  725
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             149               725
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   245  33
  6Q LOSS WILD-TYPE 672 115
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              278               787 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               33               115 
$`6Q LOSS MUTATED`
TCGA-A2-A0CQ TCGA-A2-A25A TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A8-A06T TCGA-A8-A08F 
       88.60       107.70        11.28        11.97        53.06        33.01 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AO-A0JI 
        1.02        49.05        45.07        29.98        16.57        50.24 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-BH-A1F5 TCGA-E2-A1BC TCGA-E2-A1L8 
       17.79         2.56        32.91        89.16        16.47        73.64 
TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-LL-A740 TCGA-S3-AA12 TCGA-3C-AAAU 
       50.07        15.68        75.02        14.50        18.87       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SN TCGA-A2-A04R 
      131.67        48.46         9.96        43.43        39.32       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       73.84        87.25       101.98       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0SV 
        5.19        98.99        25.22        80.28        35.05        27.12 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FV 
       49.84        20.52        18.90        20.75        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV 
       17.36        42.44       105.34        39.65        33.93        32.75 
TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IY 
       56.28        21.30        31.73        25.15        20.61        11.34 
TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07J 
       13.02        26.01         1.02        53.98         9.01        12.00 
TCGA-A8-A07S TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A097 
        7.99        19.96        12.00        37.05        31.00        12.00 
TCGA-A8-A09A TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 
        9.99        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        73.91        73.05        99.35 
TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3TM TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62Y 
       26.04        32.45        25.05        29.26        16.80        17.42 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AS TCGA-AN-A0FF 
       20.19         1.32         0.23         1.78         0.33         5.65 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03R TCGA-AO-A03T 
        0.33         0.33         5.59        66.77        68.75        69.83 
TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG TCGA-AO-A0JJ 
       21.40        37.48        20.32        22.36        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A1KR TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U2 
       55.33        82.62        98.33         5.26       107.24        83.87 
TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 
       94.29        50.89         2.76       112.77       105.30        93.30 
TCGA-AR-A255 TCGA-AR-A256 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RG TCGA-B6-A0RO 
       71.05        93.83       275.87       233.62        68.45       162.05 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU 
      282.90        79.46       113.79        43.59       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 
       85.35        68.12        71.15        62.93        81.44        70.22 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BW TCGA-BH-A0C0 
       21.70        61.68        75.48        74.14        77.95        41.75 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 
       89.06        77.98        38.01        78.28        15.65        14.30 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW 
       63.32        15.16        23.08        52.96        26.50        51.32 
TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L 
       27.25        23.93        32.91        35.93        90.84        26.66 
TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1FC TCGA-BH-A1FE 
       66.05        69.93       113.82        42.28       114.15        74.73 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A42V TCGA-BH-A8FZ TCGA-C8-A12M 
       63.35        45.63        28.14        20.88        18.87        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HO 
       12.66        11.77        12.66        12.46        11.34        12.33 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ 
       12.95        16.87        24.56        13.02        13.41        19.46 
TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       13.48        55.50        18.15        18.90        53.00        18.97 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM 
       19.40        27.58        18.15        15.22        19.92        17.69 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27R TCGA-D8-A27T 
       16.64        12.99        15.52         9.93        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10F 
       12.26        12.66        34.42        46.59        40.11        28.87 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       34.26        69.96        23.24        20.71        21.63        12.92 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IL 
       19.56        56.94        76.57        37.25        77.65         3.88 
TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       28.90        43.04        17.69        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R6 
       34.16        36.56        35.77        24.82        28.27        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A229 
       45.01        32.09        21.27        46.59        47.64        37.74 
TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A5UO 
       39.09         1.94         7.13        29.72        30.44        25.81 
TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 
       26.40        18.90        13.25        28.77        29.85        41.13 
TCGA-EW-A1P5 TCGA-EW-A3E8 TCGA-EW-A6S9 TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DC 
       23.11        34.03        15.22        33.21        79.10        83.34 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM 
       69.30        66.38        21.24        13.28        10.62        15.32 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO 
       19.53        19.59        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        18.81        18.48        21.07 
TCGA-S3-AA14 TCGA-UU-A93S 
       17.39         3.81 

$`6Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 
       48.56        48.36        19.20        63.12        36.13        19.56 
TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
       38.30        23.61        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S 
       22.32        11.05        29.03        19.99        15.06        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       33.01        17.95        19.79        14.53        19.33        13.71 
TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
        5.65        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A8FY 
       73.35        81.63        54.05        32.58        21.44         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A2P5 TCGA-EW-A1P3 
       10.42        21.14        14.79        50.79        26.99        52.96 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-OL-A5RU TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALK 
       40.08        13.94        11.41        52.96       108.07        47.61 
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
       11.44         8.52        14.37        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68        31.79         7.96        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      143.15        18.02        78.41        55.43       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       118.45 
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-A1FX TCGA-A2-A1FZ 
       18.61        19.33        48.46        31.73        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D 
       20.25        19.20        16.47        52.47        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY 
       10.59        36.23        91.07        29.98        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         7.30        24.39        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13H 
       37.45        35.67        33.11        29.79        20.19        29.56 
TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       23.74        10.59        10.29        13.41        14.70        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-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        17.98        31.00        17.03        43.00        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-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-A08L TCGA-A8-A08P TCGA-A8-A08R 
        0.99        38.01        28.96         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
      112.08        43.00        40.01        30.97        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       12.00        50.04        25.02        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       12.00        19.04         0.99        38.04        19.23        22.95 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72        22.26        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH 
       87.12        74.14        33.04        19.33        14.66         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W7 
       16.31        14.83        22.19        24.13        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79        14.96        11.44        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OS 
       12.26         1.68         8.22         0.03         1.12         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.33         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-A0AT 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        7.04         0.36         0.33         0.33         5.36         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-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03U 
        5.33        80.28        61.35        81.63        95.70        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA 
       44.42        32.78        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-A0JM 
       50.70        50.86        72.00        76.77        65.10        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        61.87        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT 
      130.09        15.62        32.52       140.55        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
      120.33        99.78       118.59       104.28        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      102.84        50.96        98.76        98.66        89.00        99.62 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29        11.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.52       146.50       112.37        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
      165.76       129.07       140.88       255.68       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       263.28       102.77       140.28       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       169.51        97.48       188.68        18.35        21.01 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 
      101.52        73.51        37.87         7.07        74.99        18.84 
TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 
      103.63        59.84        20.45        25.55        63.09        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS 
       43.53        61.51        74.89        72.23        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.75        49.94        74.14        46.39        90.97        81.73 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       67.10        29.98        13.91         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 
       67.86        70.88        16.27         4.41        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        81.83        24.49        31.00        30.35        10.78 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK 
       63.39        53.26        24.56        41.00        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        50.79         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18J 
       24.95        42.35        44.81        23.05         4.90        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
       72.56        37.74        30.28        55.63        37.55         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        51.16        91.99        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN 
      120.62        33.17       122.83        33.99        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       53.98        55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 
       18.64        23.51         9.63         5.26        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92        12.49        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        12.33        12.95        20.25        12.53        12.36 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
       15.45        16.70         0.03         9.76        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       12.95        12.49        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        19.20        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       15.78        12.03        14.01        20.09        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-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-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        21.83        14.50        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y2 
       16.31        15.16        43.04        16.54        15.32        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-A27V 
       48.03        16.41        13.48        17.06         1.61        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        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O 
       27.52        40.41        37.51        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        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 
       32.02        31.96        69.34        18.51        63.62        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        25.05        23.34        22.82        17.29 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       59.18        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       19.66        24.59        75.81       106.75       102.61         8.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       34.55        43.56         8.28        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       34.29        34.82        36.20        39.55        41.62        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       25.84        18.94         9.86        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        3.02        48.23        40.24         1.12        46.65         6.58 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       34.45        32.05        42.25        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A 
       40.73        40.50        20.12         0.69        38.99        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       12.33         9.47        38.07        32.91        30.18        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       23.84        26.70         0.79        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
        8.48        18.21        16.57        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       40.41        39.78        29.82        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-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        17.52        23.51        16.77        24.99        31.30 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH 
        7.40       109.87        59.57       216.76        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       38.20        43.73        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YL 
       62.47        11.84        11.57         7.10        32.75        17.06 
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-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 
        7.46        12.36        17.49        27.91         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        34.92        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-A66N TCGA-OL-A66P TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE 
       41.92        26.04        14.07         8.91        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26         9.93        20.68        19.27        13.84 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.26        17.03        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           282.90            281.29 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            28.82             27.85 
[1] "0.2 - 282.9 (28.8)" "0.0 - 281.3 (27.9)"
[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        2        0        88        75
  6Q LOSS WILD-TYPE      69       58        4        6       264       178
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  6Q LOSS MUTATED           0         39          8         13        5       4
  6Q LOSS WILD-TYPE         2        116         19         52       15       9
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 20                69
  STAGE IA                25                58
  STAGE IB                 2                 4
  STAGE II                 0                 6
  STAGE IIA               88               264
  STAGE IIB               75               178
  STAGE III                0                 2
  STAGE IIIA              39               116
  STAGE IIIB               8                19
  STAGE IIIC              13                52
  STAGE IV                 5                15
  STAGE X                  4                 9
[1] 12  2
[1] TRUE
[1] "dimension of 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    79 158  31  11
  6Q LOSS WILD-TYPE 195 467 106  29
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              79               195
  T2             158               467
  T3              31               106
  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
  6Q LOSS MUTATED   122 105  30  18
  6Q LOSS WILD-TYPE 384 253  89  59
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0             122               384
  N1             105               253
  N2              30                89
  N3              18                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   234   6
  6Q LOSS WILD-TYPE 655  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    234    6
  6Q LOSS WILD-TYPE  655   16
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             234               655
  1               6                16
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   279   1
  6Q LOSS WILD-TYPE 788  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    279    1
  6Q LOSS WILD-TYPE  788   11
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             279               788
  MALE                 1                11
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    96 163
  6Q LOSS WILD-TYPE 341 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     96  163
  6Q LOSS WILD-TYPE  341  384
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               96               341
  YES             163               384
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q LOSS MUTATED                            0                           206
  6Q LOSS WILD-TYPE                          1                           562
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q LOSS MUTATED                               44                   1
  6Q LOSS WILD-TYPE                            157                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q LOSS MUTATED                       1                               10
  6Q LOSS WILD-TYPE                     8                               20
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  6Q LOSS MUTATED                    7             11
  6Q LOSS WILD-TYPE                 10             35
D53V9, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                206               562
  INFILTRATING LOBULAR CARCINOMA                44               157
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)              10                20
  MUCINOUS CARCINOMA                             7                10
  OTHER, SPECIFY                                11                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"
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                          51   184
  6Q LOSS WILD-TYPE                       130   560
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                     51               130
  WHITE                                        184               560
[1] 4 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     8 224
  6Q LOSS WILD-TYPE  31 650
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8  224
  6Q LOSS WILD-TYPE   31  650
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                31
  NOT HISPANIC OR LATINO             224               650
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    95  14
  7P LOSS WILD-TYPE 822 134
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              109               956 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               134 
$`7P LOSS MUTATED`
TCGA-A7-A0CD TCGA-A7-A26I TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       38.30        21.73        29.03        33.01        33.01        33.01 
TCGA-AC-A62X TCGA-AQ-A54N TCGA-LL-A5YP TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO 
       13.71         2.56        14.79         9.96        31.79        28.01 
TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0SX 
       73.84        75.25        25.22        79.76        35.05        50.43 
TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A4RX TCGA-A2-A4S3 
       49.84        23.77        17.36        19.20        24.39        21.90 
TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A079 
       30.61        29.79        10.42        13.02        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A092 TCGA-A8-A09Q 
       43.00        18.97        38.01         9.99        30.97        25.02 
TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH TCGA-AN-A04C TCGA-AN-A0AM 
       19.04        27.02        22.95        33.04         1.78         0.16 
TCGA-AN-A0AS TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 
        0.33         0.33         0.33         0.33        80.28        20.32 
TCGA-AO-A0JE TCGA-AO-A12F TCGA-AO-A1KS TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AQ 
       76.77        60.56        11.51       107.21       108.36        99.32 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RS 
       71.05        54.21       233.62       165.76        68.45       100.70 
TCGA-B6-A0WY TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0HI 
      113.79        74.99        68.12        61.51        41.75        20.38 
TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1F8 TCGA-BH-A42T 
       32.91        26.66        55.63        51.39        25.08        10.52 
TCGA-C8-A1HF TCGA-C8-A1HM TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JE 
       10.92        12.33        16.70        19.20        17.49        18.90 
TCGA-D8-A1JM TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK 
       19.40        14.70        18.58        27.58        18.15        14.50 
TCGA-D8-A1XQ TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1L7 
       16.41        13.48        18.51        12.92        14.07        60.36 
TCGA-E9-A1N6 TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 
       22.29         6.58        38.37        40.73         0.69         1.94 
TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1PC TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD 
       23.84        26.40         6.15        16.77        24.99        33.21 
TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LL-A7T0 TCGA-OL-A5RY TCGA-S3-A6ZG 
      109.87        85.15        69.30        12.36        24.72        18.48 
TCGA-S3-AA10 
       19.27 

$`7P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E 
       22.32        11.28        11.97        11.05        53.06        19.99 
TCGA-A8-A084 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       15.06        17.95         1.02        49.05        45.07        29.98 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT 
       16.57        19.79        14.53        19.33        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
        5.65        32.91        19.20        98.33        17.23        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       57.27        73.35        81.63        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O 
       89.16         9.70        10.42        21.14        14.79        50.79 
TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       16.47        73.64        50.07        26.99        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       18.02        78.41       121.94        87.25       101.98        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      136.73        99.12        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       77.19         5.19        98.99       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        33.76        61.58       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
      118.45        74.40        72.00        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-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52        17.13         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-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-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       31.73        23.47        60.72        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        26.96        21.14        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-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       25.15        29.56        23.74        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.29        13.41        14.70        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       21.17        17.92        14.73        12.10        10.72        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
        9.37         8.75        13.02         1.02        17.98        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       26.01         1.02        53.98        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-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-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
       28.96        19.96        12.00        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 
        0.99       112.08        43.00        40.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
        9.99         9.99        12.00        50.04        33.07         1.02 
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-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        19.23 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       24.79        29.26        16.80        14.96        11.44        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-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-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-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.36         7.46         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         6.90         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         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         5.33         5.59 
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        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        44.42        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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       72.00        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       97.08        61.87        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       133.22        83.87       134.14       125.16       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      103.86        97.68        96.00        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        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       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       85.64        93.83       166.42        20.25        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.52       146.50       112.37        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       129.07       140.88       255.68       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       169.51        97.48       188.68        79.46 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.01       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.55        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A409 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        62.93        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       81.44        39.55        39.16        70.22        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       37.22        32.02        18.21        43.53        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       77.75        49.94        77.95        74.14        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        81.83        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       23.08        41.00        52.96        26.50         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-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN 
       30.28        37.55        66.05         7.36        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-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB 
       49.58        17.69        25.81        31.53        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       122.83        33.99        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        53.98        55.50        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        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       36.79        20.12       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26        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-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51        12.59        12.59        12.92        12.46        12.49 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN 
       12.33        11.34        11.28         0.16        12.03        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       16.87         0.03         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
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-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF 
       14.17        16.50        55.50        15.78        18.15        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.38        21.01        12.20        13.32        17.79        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-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        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        48.03        16.41        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        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        12.66        25.22        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        75.98        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        69.34        63.62        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        25.05        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        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        11.05        19.56        56.94        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       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        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
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        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        41.03        41.72        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       38.99         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       38.07        32.91        30.18        30.44        23.90        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        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-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-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-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-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 
       17.52        23.51        15.22        31.30         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
      216.76        79.10        83.34        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       32.75        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 
        2.63        16.08        15.68         7.46        19.53        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ 
       31.99        58.62        34.92        36.36        28.87        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-AA11 TCGA-S3-AA14 
        9.93        18.81        21.07        20.68        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.16              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           233.62            282.90 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            24.72             28.93 
[1] "0.2 - 233.6 (24.7)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         7        8        1        2        43        24
  7P LOSS WILD-TYPE      82       75        5        4       309       229
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  7P LOSS MUTATED           1         16          5          3        0       0
  7P LOSS WILD-TYPE         1        139         22         62       20      13
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                 8                75
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               43               309
  STAGE IIB               24               229
  STAGE III                1                 1
  STAGE IIIA              16               139
  STAGE IIIB               5                22
  STAGE IIIC               3                62
  STAGE IV                 0                20
  STAGE X                  0                13
[1] 12  2
[1] TRUE
[1] "dimension of 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  73  11   5
  7P LOSS WILD-TYPE 252 552 126  35
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              22               252
  T2              73               552
  T3              11               126
  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    60  28  18   4
  7P LOSS WILD-TYPE 446 330 101  73
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              60               446
  N1              28               330
  N2              18               101
  N3               4                73
[1] 4 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   101   0
  7P LOSS WILD-TYPE 788  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    101    0
  7P LOSS WILD-TYPE  788   22
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0             101               788
  1               0                22
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   110   1
  7P LOSS WILD-TYPE 957  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    110    1
  7P LOSS WILD-TYPE  957   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE             110               957
  MALE                 1                11
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    39  61
  7P LOSS WILD-TYPE 398 486
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     39   61
  7P LOSS WILD-TYPE  398  486
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               39               398
  YES              61               486
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P LOSS MUTATED                            0                            95
  7P LOSS WILD-TYPE                          1                           673
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P LOSS MUTATED                                5                   2
  7P LOSS WILD-TYPE                            196                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P LOSS MUTATED                       2                                3
  7P LOSS WILD-TYPE                     7                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  7P LOSS MUTATED                    0              4
  7P LOSS WILD-TYPE                 17             42
D54V9, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 95               673
  INFILTRATING LOBULAR CARCINOMA                 5               196
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                27
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 4                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"
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                          25    65
  7P LOSS WILD-TYPE                       156   679
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                     25               156
  WHITE                                         65               679
[1] 4 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     2  89
  7P LOSS WILD-TYPE  37 785
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   89
  7P LOSS WILD-TYPE   37  785
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO              89               785
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED   101  17
  7Q LOSS WILD-TYPE 816 131
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              118               947 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               131 
$`7Q LOSS MUTATED`
TCGA-A7-A0CD TCGA-A7-A26I TCGA-A8-A06U TCGA-A8-A08S TCGA-A8-A09I TCGA-E2-A1BC 
       38.30        21.73        29.03        33.01        45.07        16.47 
TCGA-E2-A1L8 TCGA-LL-A5YP TCGA-5T-A9QA TCGA-A1-A0SO TCGA-A2-A0CT TCGA-A2-A0D4 
       73.64        14.79         9.96        28.01        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-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A6VX TCGA-A8-A06O 
       19.20        24.39        30.61        29.79        10.42        13.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A08B 
       17.03        53.98         9.01        18.97        14.01        38.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 
       30.97         9.99         0.99        12.00        19.04        27.02 
TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62V TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A0AJ 
       22.95        33.04        11.44         0.62         1.78         9.96 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT 
        0.16         0.33         7.04         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A1KS TCGA-AR-A0U2 TCGA-AR-A0U4 
       80.28        20.32        76.77        11.51        83.87       107.21 
TCGA-AR-A24H TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0IC TCGA-B6-A0IO 
      160.90        50.96        71.05        54.21        50.70       165.76 
TCGA-B6-A0RS TCGA-B6-A0WY TCGA-B6-A408 TCGA-BH-A0AZ TCGA-BH-A0BG TCGA-BH-A0DZ 
      100.70       113.79        68.12        63.09        61.51        16.27 
TCGA-BH-A0HI TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U 
       20.38        44.81        32.91        26.66        55.63        51.39 
TCGA-BH-A1EV TCGA-BH-A1FN TCGA-BH-A42T TCGA-BH-A5J0 TCGA-C8-A12W TCGA-C8-A138 
       12.00        72.07        10.52        23.51        12.66        12.49 
TCGA-C8-A1HF TCGA-C8-A1HM TCGA-D8-A1JE TCGA-D8-A1JJ TCGA-D8-A1JU TCGA-D8-A1X5 
       10.92        12.33        18.90        20.09        14.70        18.58 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A27M 
       27.58        18.15        14.50        16.41        12.99        13.48 
TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15M TCGA-E2-A1L7 TCGA-E2-A1LB TCGA-E9-A1N6 
       18.51        12.92        11.05        60.36        75.81        22.29 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A22B 
        2.56         6.12        48.23        40.24         6.58        38.37 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A54Y TCGA-E9-A5UP 
        0.69         1.94        24.56        38.07        23.84        26.40 
TCGA-EW-A1PC TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-LL-A7SZ 
        6.15        16.77        33.21       109.87        85.15        19.53 
TCGA-OL-A5RY TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       24.72        18.48        20.68        19.27 

$`7Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        23.61        31.36        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E 
       22.32        11.28        11.97        11.05        53.06        19.99 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       15.06        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       50.24        17.79         5.65         2.56        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 
       98.33        17.23        66.15        57.27        73.35        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 
       21.14        14.79        50.79        50.07        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G 
       25.05        14.50        40.08        18.87        13.94        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       52.96       108.07       133.05       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       87.25       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
      114.81        92.48       107.93        77.19         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-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72       134.40        80.28       118.45        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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
        8.38        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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       22.45        20.25        16.47        52.47        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        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         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-A13H 
       35.67        33.11        31.73        20.19        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       14.70        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.73        12.10        10.72        10.29         9.37         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       43.00        18.97        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
       36.95        13.02         0.99        28.96        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       37.05         9.99        31.00        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        40.01        41.98        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       50.04        33.07         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
       15.02        14.01        13.02        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04        19.23        73.91         5.72        22.26        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        74.14        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
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 
        7.46         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         6.90         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         5.36         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        69.83        58.95        44.42 
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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        62.04        55.33        71.80       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03       102.31        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       70.42        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       61.87        82.62        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        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 
      133.22       134.14       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       94.29        61.28        86.53        86.43        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
      112.77        97.84       105.27       102.84       105.30        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       98.66        89.00        99.62        93.30        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG 
      281.29        11.90       275.87       129.57        65.52       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       233.62        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.28        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.55        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        85.35        74.99        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 
       71.15        62.93        59.84        20.45        25.55        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        84.13        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        43.53        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        81.73        77.98        67.10        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        70.88         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        81.83        24.49        31.00        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        63.39        53.26        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         4.90        35.93 
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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        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        36.82        36.79        20.12       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        18.64         9.63         5.26        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-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.16        13.51        12.59        12.59        12.92        12.46 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN 
       12.33        11.34        11.28         0.16        12.03        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       16.87        16.70         0.03         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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 
       56.81        20.88        13.25        20.58        13.97        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        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        12.03        53.00        14.01        18.97 
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-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       13.32        17.79        16.73        25.74        23.90        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-A1XV TCGA-D8-A1XW 
       55.30        15.85        16.31        16.64        15.16        43.04 
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        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41        17.06         1.61        10.09        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-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        75.98        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        69.34        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A 
       23.24        19.43        21.04        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       53.92         9.04        20.58        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LH 
       11.08        54.18        19.66        24.59        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        38.76        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        34.16        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       41.62        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA 
       24.82        28.27        34.95         3.02        11.15        45.01 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       32.09         1.12        46.65        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       34.45        32.05        42.25        37.74        39.09        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 
       41.72        40.73        40.50        20.12        38.99         7.13 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.33        29.72         9.47        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90        26.70         0.79        25.81        27.85        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-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-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        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-EW-A6S9 TCGA-EW-A6SB 
       34.03        17.49        17.52        23.51        15.22        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       31.30         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-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        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       21.24         7.10        13.28        10.62        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68         7.46        12.36        19.59        17.49        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-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        36.36        28.87        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        18.81 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S 
       21.07        13.84        17.39        17.26        17.03         3.81 
TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        29.03        15.35        16.04       107.05 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.16              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           165.76            282.90 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            22.01             29.56 
[1] "0.2 - 165.8 (22.0)" "0.0 - 282.9 (29.6)"
[1] "hr=" "1.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         7       11        1        1        41        27
  7Q LOSS WILD-TYPE      82       72        5        5       311       226
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  7Q LOSS MUTATED           1         20          4          4        1       2
  7Q LOSS WILD-TYPE         1        135         23         61       19      11
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                11                72
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               41               311
  STAGE IIB               27               226
  STAGE III                1                 1
  STAGE IIIA              20               135
  STAGE IIIB               4                23
  STAGE IIIC               4                61
  STAGE IV                 1                19
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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  78  12   5
  7Q LOSS WILD-TYPE 249 547 125  35
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              25               249
  T2              78               547
  T3              12               125
  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
  7Q LOSS MUTATED    58  35  18   7
  7Q LOSS WILD-TYPE 448 323 101  70
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              58               448
  N1              35               323
  N2              18               101
  N3               7                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED   106   1
  7Q LOSS WILD-TYPE 783  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    106    1
  7Q LOSS WILD-TYPE  783   21
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0             106               783
  1               1                21
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED   118   2
  7Q LOSS WILD-TYPE 949  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    118    2
  7Q LOSS WILD-TYPE  949   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE             118               949
  MALE                 2                10
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    43  64
  7Q LOSS WILD-TYPE 394 483
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     43   64
  7Q LOSS WILD-TYPE  394  483
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               43               394
  YES              64               483
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q LOSS MUTATED                            0                            99
  7Q LOSS WILD-TYPE                          1                           669
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q LOSS MUTATED                               11                   0
  7Q LOSS WILD-TYPE                            190                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q LOSS MUTATED                       2                                4
  7Q LOSS WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  7Q LOSS MUTATED                    0              4
  7Q LOSS WILD-TYPE                 17             42
D55V9, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 99               669
  INFILTRATING LOBULAR CARCINOMA                11               190
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                26
  MUCINOUS CARCINOMA                             0                17
  OTHER, SPECIFY                                 4                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"
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                          22    74
  7Q LOSS WILD-TYPE                       159   670
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                     22               159
  WHITE                                         74               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"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  96
  7Q LOSS WILD-TYPE  38 778
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   96
  7Q LOSS WILD-TYPE   38  778
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                38
  NOT HISPANIC OR LATINO              96               778
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   329  63
  8P LOSS WILD-TYPE 588  85
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              392               673 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63                85 
$`8P LOSS MUTATED`
TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A7-A3J1 TCGA-A8-A06T 
       19.20        63.12        36.13        19.56        11.28        53.06 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09K TCGA-AC-A3W5 
       19.99        15.06        33.01        33.01        29.98        16.57 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-BH-A0B6 TCGA-BH-A18H 
       17.79         5.65        98.33        17.23        81.63        21.44 
TCGA-C8-A1HL TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1P3 TCGA-LL-A440 TCGA-LL-A50Y 
       10.42        73.64        50.07        52.96        24.95        25.05 
TCGA-S3-AA17 TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P 
       13.94        48.46        11.44        39.32        28.01        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       78.41        73.84        87.25        99.12       114.81        92.48 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EU TCGA-A2-A0EV 
        5.19       107.93        34.55        25.22        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       61.94        24.72        50.43        17.52        17.13        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       20.75        21.67        19.33        23.77        17.36        60.72 
TCGA-A2-A25D TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       18.15        91.07        29.98        50.37        50.83         7.30 
TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26J TCGA-A7-A3IZ 
       21.90        37.45        31.73        20.19        20.61        10.59 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06R 
       21.17        17.92        14.73        12.10        13.02        17.98 
TCGA-A8-A075 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A085 TCGA-A8-A08G 
       17.03        32.05        10.98         7.99        36.95        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09D TCGA-A8-A09N 
       37.05        31.00        43.00        12.00        50.04         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A7 TCGA-AC-A2FO TCGA-AC-A2QH 
       25.02         8.98        19.04         0.99        74.14        33.04 
TCGA-AC-A3TN TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A041 
       14.99        16.80        14.96         8.22        20.19         0.23 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        0.62         2.96         1.78         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.44         6.90         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         0.33         0.33        66.77        81.63        95.70 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL 
       53.03        21.53        50.70        76.77        26.24        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR 
       71.80       115.27       108.72        82.68        53.88        82.62 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      130.09        15.62       140.55        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       98.93        64.83        55.86       133.22        83.87       134.14 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AW TCGA-AR-A1AX 
      101.00       103.86        93.90        37.81        86.53        86.43 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z 
      160.90        50.89        94.22       102.84       105.30        98.66 
TCGA-AR-A250 TCGA-AR-A2LE TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 
       89.00       166.42        10.59        77.62       143.38        11.90 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RG 
      146.50       233.62        18.77       127.33       140.88        68.45 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WY 
      100.70       282.90        97.48       188.68        18.35       113.79 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C 
       68.94        58.55       139.17        68.12        18.84        71.15 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP 
       59.84        25.55        84.13        61.51        74.89        75.48 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG 
       76.60        49.94        74.14        41.75        90.97        67.10 
TCGA-BH-A0DL TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 
       78.28         9.63        24.49        31.00        63.32        23.08 
TCGA-BH-A0HK TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W5 
        5.85        51.32        27.25        50.79        23.93        42.35 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18S 
       32.91        35.93        20.12        90.84        37.74        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EY 
        7.36        51.39        51.16        69.93        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FN 
       25.81        31.53        25.08        33.17        33.99        72.07 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V 
       55.50        28.14        38.60        57.83       130.16        20.88 
TCGA-BH-A8FZ TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Z 
       18.87         9.44        11.77        11.77        11.77        12.56 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HG 
       13.51        12.59        12.59        12.46        12.49        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26W 
       11.28        12.03        12.33        12.95        12.33        12.53 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.76        24.56        14.43        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A145 
       19.46        56.81        20.88        13.25        14.17        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       14.17        17.49        18.15        53.00        20.09        20.12 
TCGA-D8-A1JT TCGA-D8-A1X8 TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XQ 
       13.32        25.74        17.16        21.83        17.69        16.41 
TCGA-D8-A1XS TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L 
       16.31        15.52        14.24        16.04        13.05        16.41 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A105 
       13.48        10.09        12.26        18.51        16.18        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14S TCGA-E2-A14T 
       27.52        40.41        40.11        47.15        33.17        75.98 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A15A 
       34.26        32.02        31.96        18.51        63.62        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15R 
       22.82        20.71        12.92        53.92         9.04        56.94 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       53.62        32.35        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A1LI 
       33.70        60.99        54.18        60.36        28.90       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 
        8.75        43.04         8.28        38.76        17.69        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1NI 
       34.16        36.20        41.62        35.24        18.94         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       34.95         3.02        48.23        46.65         6.58        46.59 
TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       34.45        37.74        39.09        38.37        41.03        41.72 
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-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE 
       22.82        29.85        40.41         7.86        18.90        10.52 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3U0 
       14.43        19.96        55.00        52.73        25.91        17.49 
TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        24.99        33.21       109.87        59.57       216.76 
TCGA-GM-A3NW TCGA-GM-A3XL TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
      110.50        69.30        13.55        62.47        11.84        11.57 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FR 
        7.10        13.28        32.75        15.32        14.70        16.08 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       12.36        19.59        17.49        24.72        22.32        20.38 
TCGA-OL-A66J TCGA-OL-A66P TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZH 
       65.62        14.07        47.01        64.21        86.96        21.07 
TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.39        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

$`8P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A0CQ TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G 
       48.56        48.36        88.60       107.70        38.30        23.61 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A426 
       31.36        24.26        23.80        21.73        22.32        11.97 
TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       11.05        29.03        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
       45.07        19.79        14.53        19.33        13.71        50.24 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
        2.56        32.91        19.20        66.15        57.27        73.35 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 
       54.05        32.58        89.16         9.70        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.79        16.47        26.99        15.68        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A442 TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       13.22        29.23        14.79        14.50        40.08        18.87 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK 
       11.41        52.96       108.07       133.05       131.67        47.61 
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-A0SQ 
       47.24        20.88        13.68        31.79         7.96        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM 
      143.15       121.94       101.98        55.43       136.73        24.79 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        77.19        75.25        98.99        56.81        67.33 
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       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0ST 
       79.76        74.40        72.00        35.05        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T2 TCGA-A2-A0T4 
       54.64        27.12        44.88        44.28         8.38        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-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-A25B 
       22.45        20.25        19.20        16.47        52.47        42.44 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       17.19       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY 
       32.75        56.28        47.31        35.93        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        26.96        21.14        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H 
       30.61        35.67        33.11        29.79        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       23.74        11.34        10.29        13.41        14.70        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       13.74        14.50        10.72        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        8.75        13.02         1.02        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       12.00         9.99         8.98        24.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I 
       18.05        13.02         0.99        38.01        28.96        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00         0.99       112.08        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09V 
       41.98         9.99         9.99        12.00        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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A2QJ 
       90.71        60.92        87.12        26.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62V 
       25.05        15.48        23.24        24.79        29.26        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       17.42        18.67        13.58        12.26         1.68         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.33         0.33 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FF 
        1.71         9.96         7.36         7.46         0.33         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FW 
        7.96         7.00         7.59         7.17         7.04         0.36 
TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV 
        0.33        12.33         0.30         0.33         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        69.83        58.95 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JJ 
       20.32        22.36        50.86        72.00        65.10        62.04 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
      113.62       106.78       108.03       102.31        98.27        70.42 
TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       60.56        40.57        20.45        97.08        61.87        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ 
       24.79        26.93        32.52        98.33         5.26       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AL TCGA-AR-A1AN 
       65.36       107.21       125.16       108.36        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24M 
       86.07        99.32        94.29        61.28        33.73       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
      105.27        50.96        98.76        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       71.05        93.83        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I5 
       38.17        39.39        40.54        33.30        38.96       281.29 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IN 
      275.87       129.57        50.70        65.52       112.37        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      165.76       129.07       255.68       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.28        89.46 
TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      169.51        79.46        21.01       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX 
       28.27        43.59       101.52        73.51       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW 
        7.07        85.35        74.99       103.63        62.93        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 
       63.09        81.44        39.55        39.16        70.22        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       37.22        32.02        18.21        43.53        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C1 
       72.23        74.14        85.87        77.75        77.95        46.39 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       89.06        81.73        77.98        38.01        29.98        13.91 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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        81.83 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50        20.38         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A0WA 
       36.85        12.89         5.59        24.95        44.81        23.05 
TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
        4.90        26.66        72.56        30.28        55.63        37.55 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        12.00        49.58 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
       97.48       120.62       114.15        74.73       122.83        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O 
       55.00        45.63        53.98        26.14        83.31        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A5J0 
       36.79        20.12        10.52       110.60        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12Q 
        9.63         5.26        21.76        11.93        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 
       12.66        12.66        12.66        12.66        48.53        12.16 
TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26X 
       12.92        12.33        10.92         0.16        20.25        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 
       12.95        15.45        16.87        16.70         0.03        33.99 
TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.02        20.58        13.97        19.20        16.50        55.50 
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-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-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        23.90        27.58        18.15        12.39 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        14.50        19.92        55.30        15.85 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
        9.93        14.14        17.42        13.45        14.43        48.03 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
       17.06         1.61        13.08        12.53        33.37        21.67 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10E 
       12.66        25.22        34.42        46.59        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U 
       28.87        44.68        40.96        38.24        38.60        43.33 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       69.34        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A159 TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15L 
       25.05        17.29        21.63        18.21        55.63        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       11.05        19.56        14.07        51.39        76.57        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       33.01        28.50        37.25        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       22.19        11.08        19.66        24.59        75.81       106.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 
       34.55        43.56        30.61        34.92        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       32.88        36.82        36.56        39.55        35.77        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA 
       24.82        28.27         2.56         6.12        11.15        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
       32.09        40.24         1.12        21.27        47.64        32.05 
TCGA-E9-A228 TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 
       42.25        40.73        40.50        20.12        38.99         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       27.85        12.20         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       16.57        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-EW-A6S9 TCGA-EW-A6SA 
       34.55        22.09        34.03        17.52        15.22        16.77 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       31.30         7.40        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY 
       85.15        86.96       115.69       106.06       101.62        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-LD-A66U 
       43.73        66.38        72.03        18.12         2.60        21.24 
TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       10.62        17.06        14.47        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        7.46        19.53        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        34.92        36.36        28.87 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        23.47        41.92        42.77        26.04        17.36 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PL-A8LX TCGA-PL-A8LY 
       28.21        19.73        40.11         8.91         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        20.68        19.27        13.84 
TCGA-S3-AA15 
       17.26 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.16              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           282.90            281.29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           28.965            27.910 
[1] "0.2 - 282.9 (29.0)" "0.0 - 281.3 (27.9)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED        31       32        2        1       128        95
  8P LOSS WILD-TYPE      58       51        4        5       224       158
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  8P LOSS MUTATED           0         59          9         25        6       5
  8P LOSS WILD-TYPE         2         96         18         40       14       8
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 31                58
  STAGE IA                32                51
  STAGE IB                 2                 4
  STAGE II                 1                 5
  STAGE IIA              128               224
  STAGE IIB               95               158
  STAGE III                0                 2
  STAGE IIIA              59                96
  STAGE IIIB               9                18
  STAGE IIIC              25                40
  STAGE IV                 6                14
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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   102 235  41  16
  8P LOSS WILD-TYPE 172 390  96  24
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1             102               172
  T2             235               390
  T3              41                96
  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   183 129  49  28
  8P LOSS WILD-TYPE 323 229  70  49
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             183               323
  N1             129               229
  N2              49                70
  N3              28                49
[1] 4 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   6
  8P LOSS WILD-TYPE 555  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    334    6
  8P LOSS WILD-TYPE  555   16
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             334               555
  1               6                16
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   391   3
  8P LOSS WILD-TYPE 676   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    391    3
  8P LOSS WILD-TYPE  676    9
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             391               676
  MALE                 3                 9
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   162 202
  8P LOSS WILD-TYPE 275 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    162  202
  8P LOSS WILD-TYPE  275  345
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              162               275
  YES             202               345
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P LOSS MUTATED                            1                           313
  8P LOSS WILD-TYPE                          0                           455
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P LOSS MUTATED                               50                   2
  8P LOSS WILD-TYPE                            151                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P LOSS MUTATED                       1                                8
  8P LOSS WILD-TYPE                     8                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  8P LOSS MUTATED                    3             16
  8P LOSS WILD-TYPE                 14             30
D56V9, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                313               455
  INFILTRATING LOBULAR CARCINOMA                50               151
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             3                14
  OTHER, SPECIFY                                16                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"
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1    30
  8P LOSS WILD-TYPE                                0    30
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          71   261
  8P LOSS WILD-TYPE                       110   483
D56V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         30                30
  BLACK OR AFRICAN AMERICAN                     71               110
  WHITE                                        261               483
[1] 4 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    12 330
  8P LOSS WILD-TYPE  27 544
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12  330
  8P LOSS WILD-TYPE   27  544
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                27
  NOT HISPANIC OR LATINO             330               544
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    78  15
  8Q LOSS WILD-TYPE 839 133
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               972 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               133 
$`8Q LOSS MUTATED`
TCGA-AC-A3W5 TCGA-AQ-A0Y5 TCGA-BH-A18H TCGA-C8-A1HL TCGA-E2-A1L8 TCGA-E2-A1LG 
       16.57         5.65        21.44        10.42        73.64        50.07 
TCGA-LL-A440 TCGA-3C-AALJ TCGA-A1-A0SO TCGA-A2-A0CU TCGA-A7-A0D9 TCGA-A7-A13E 
       24.95        48.46        28.01         5.19        37.45        20.19 
TCGA-A7-A26J TCGA-A7-A4SF TCGA-A8-A07L TCGA-A8-A097 TCGA-A8-A09D TCGA-A8-A09T 
       20.61        17.92        32.05        12.00        50.04        19.04 
TCGA-AC-A2FO TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD 
       74.14        16.80        14.96         0.23         2.96         6.44 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JL TCGA-AO-A0JM 
       95.70        32.78        53.03        21.53        55.33        71.80 
TCGA-AO-A124 TCGA-AR-A0TY TCGA-AR-A0U3 TCGA-AR-A24K TCGA-B6-A0IK TCGA-B6-A0IQ 
      115.27        55.86       134.14        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        84.13 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0EB 
       76.60        49.94        74.14        90.97        67.10        24.49 
TCGA-BH-A0EE TCGA-BH-A0W3 TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 
       31.00        23.93        66.05         7.36        69.93        25.08 
TCGA-BH-A1FD TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       33.17        38.60        11.77        12.59        12.59        12.46 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A26W TCGA-C8-A8HQ TCGA-D8-A140 TCGA-D8-A145 
       12.49        11.28        12.53        12.49        13.25        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A14V TCGA-E2-A15K 
       14.17        17.49        18.51        16.18        34.26         9.04 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1LL TCGA-E9-A1N8 TCGA-E9-A1NH TCGA-E9-A1R5 
       70.36        33.73        43.04        34.16        18.94         3.02 
TCGA-E9-A1R7 TCGA-E9-A22D TCGA-E9-A244 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A3U0 
       48.23        41.03         0.69        10.52        25.91        17.49 
TCGA-EW-A424 TCGA-LL-A8F5 TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66P TCGA-PE-A5DD 
       23.51        19.59        22.32        20.38        14.07        64.21 
TCGA-PE-A5DE TCGA-S3-A6ZH TCGA-WT-AB44 
       86.96        21.07        29.03 

$`8Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
       23.80        21.73        22.32        11.28        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S 
       53.06        29.03        19.99        15.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       33.01        17.95         1.02        49.05        45.07        29.98 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT 
       19.79        14.53        19.33        13.71        50.24        17.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
        2.56        32.91        19.20        98.33        17.23        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       57.27        73.35        81.63        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A2P5 
        9.70        21.14        14.79        50.79        16.47        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A442 
       15.68        52.96        75.02        85.35        13.22        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK 
       11.41        52.96       108.07       133.05       131.67        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       39.32        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
       24.79       114.81        92.48       107.93        77.19        75.25 
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       118.45 
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-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-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-A1G6 
       17.36        60.72        22.45        20.25        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         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-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        30.61        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY 
       29.79        31.73        25.15        29.56        23.74        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        10.29        13.41        14.70        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       14.50        21.17        14.73        12.10        10.72        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-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        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-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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09N 
       41.98         9.99         9.99        12.00        33.07         1.02 
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-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        26.04        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62V 
       14.99        15.48        23.24        24.79        29.26        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-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         0.62         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         7.46         0.16         0.33         0.33         0.33 
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         6.90 
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 
        5.36         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        69.83        58.95        44.42 
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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       62.04       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       20.45        97.08        61.87        82.62        11.51        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24        65.36       133.22        83.87       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      102.84       105.30        50.96        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       233.62       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      129.07       255.68       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       162.05       102.77       140.28        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      169.51       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KC 
      206.86       129.70       245.10        28.27        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
      101.52        73.51       139.17       170.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        74.99        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        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 
       43.53        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 
       75.48        74.14        85.87        77.75        77.95        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       46.39        89.06        81.73        77.98        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
        9.63        44.81        81.83        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        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-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       17.69        25.81        31.53        97.48       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.83        33.99        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 
       72.07        53.98        55.50        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        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      110.60        20.88        18.64        23.51         9.63         5.26 
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-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE 
       48.53        12.56        12.16        13.51        12.92        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34         0.16        12.03        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       16.70         0.03         9.76        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95        13.02        13.41        19.46        56.81        20.88 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        13.97        14.17        19.20        16.50        55.50 
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        53.00        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-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        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        43.04        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-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       21.67        12.66        25.22        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-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        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-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        55.63        53.92        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       75.81        28.90       106.75       102.61         8.75        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       43.56         8.28        30.61        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       17.69        34.82        32.88        36.82        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        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        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       11.15        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
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-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-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA 
       52.73        22.09        34.03        17.52        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       24.99        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        70.85        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-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 
        2.60        62.47        11.84        11.57        21.24         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        10.62        32.75        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       19.53        12.36        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       28.87        24.72        26.70        23.47        65.62        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-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
        8.91        47.01         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       18.48        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.03         3.81        66.84        15.35        16.04       107.05 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           140.88            282.90 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            24.95             28.44 
[1] "0.2 - 140.9 (24.9)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.4"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         4        8        0        0        27        32
  8Q LOSS WILD-TYPE      85       75        6        6       325       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  8Q LOSS MUTATED           0         12          2          6        0       2
  8Q LOSS WILD-TYPE         2        143         25         59       20      11
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  4                85
  STAGE IA                 8                75
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               27               325
  STAGE IIB               32               221
  STAGE III                0                 2
  STAGE IIIA              12               143
  STAGE IIIB               2                25
  STAGE IIIC               6                59
  STAGE IV                 0                20
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    17  61  13   2
  8Q LOSS WILD-TYPE 257 564 124  38
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              17               257
  T2              61               564
  T3              13               124
  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
  8Q LOSS MUTATED    39  39   7   6
  8Q LOSS WILD-TYPE 467 319 112  71
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              39               467
  N1              39               319
  N2               7               112
  N3               6                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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    75   0
  8Q LOSS WILD-TYPE 814  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     75    0
  8Q LOSS WILD-TYPE  814   22
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              75               814
  1               0                22
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    93   0
  8Q LOSS WILD-TYPE 974  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     93    0
  8Q LOSS WILD-TYPE  974   12
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              93               974
  MALE                 0                12
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    44  41
  8Q LOSS WILD-TYPE 393 506
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     44   41
  8Q LOSS WILD-TYPE  393  506
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               44               393
  YES              41               506
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q LOSS MUTATED                            0                            73
  8Q LOSS WILD-TYPE                          1                           695
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q LOSS MUTATED                               14                   0
  8Q LOSS WILD-TYPE                            187                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q LOSS MUTATED                       0                                1
  8Q LOSS WILD-TYPE                     9                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  8Q LOSS MUTATED                    2              3
  8Q LOSS WILD-TYPE                 15             43
D57V9, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 73               695
  INFILTRATING LOBULAR CARCINOMA                14               187
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                29
  MUCINOUS CARCINOMA                             2                15
  OTHER, SPECIFY                                 3                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"
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                          20    58
  8Q LOSS WILD-TYPE                       161   686
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                     20               161
  WHITE                                         58               686
[1] 4 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     5  77
  8Q LOSS WILD-TYPE  34 797
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5   77
  8Q LOSS WILD-TYPE   34  797
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO              77               797
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   261  48
  9P LOSS WILD-TYPE 656 100
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              309               756 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               48               100 
$`9P LOSS MUTATED`
TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-AO-A1KT 
       22.32        29.03         1.02        49.05        45.07        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A2LL TCGA-C8-A1HL TCGA-EW-A1P3 TCGA-LL-A5YP 
        5.65        32.91        66.15        10.42        52.96        14.79 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CT 
      133.05       131.67        13.68        28.01        18.02        75.25 
TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV 
       67.33        80.28        79.76        35.05        34.29        27.12 
TCGA-A2-A0SW TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH 
       44.88        17.52        20.75        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        35.93        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-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R 
       14.93        13.74        17.92        10.29        13.02        17.98 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07W 
        1.02        17.03         9.01        43.00        18.97         9.99 
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-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       12.00         9.99        12.00        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 
        8.98        19.04         0.99        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        90.71        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC 
       14.66        16.80        14.96        11.44        13.58         0.03 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       20.19         0.33         0.33         0.23         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FJ 
        1.78         9.96         7.36         7.46         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-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JA TCGA-AO-A0JD 
       66.77        44.42        52.18        26.04        21.53        72.00 
TCGA-AO-A0JE TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AQ-A1H2 
       76.77        60.56        61.87        11.51       130.09        15.62 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       98.33         5.26        84.10        75.22        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP 
      133.22        83.87       134.14       125.16       108.36        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S 
       99.32        86.53        50.89        99.78       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.30        50.96        98.66        99.62        93.30        71.05 
TCGA-AR-A2LK TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RO 
       54.21        11.90       129.57        18.77       165.76       162.05 
TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 
      102.77        79.46        18.35        85.35        68.12        18.84 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       62.93        20.45        63.09        39.55        70.22        84.13 
TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW 
       43.53        74.89        75.48        76.60        49.94        77.95 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E6 
       89.06        90.97        29.98        13.91         3.22         9.63 
TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       24.49        30.35        10.78        23.08        41.00        52.96 
TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A18U 
       50.79        23.93        90.84        26.66         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM 
       69.93       113.82        17.69        31.53        25.08        45.63 
TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-AB28 
       72.07        55.50        57.83       130.16        10.52         9.44 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X 
       11.93        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HM TCGA-C8-A26V 
       12.16        13.51        12.46        11.34        12.33        20.25 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Y 
       12.95        16.87        14.43        13.02        13.41        56.81 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ 
       20.88        14.17        13.48        15.78        53.00        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XD 
       20.12        19.40        18.58        17.79        27.58        17.16 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27F 
       16.41        16.31        16.64        16.54        14.14        16.04 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R 
       17.06        10.09        12.26        46.59        44.68        38.60 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A15A 
       75.98        32.02        31.96        18.51        69.96        23.34 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1LA TCGA-E2-A1LB 
       20.71        21.63        12.92        14.07        24.59        75.81 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA 
      106.75       102.61         8.75        34.92        36.20        36.56 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 
       35.24         9.86        24.82        34.95         6.12        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        32.09        40.24        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A5UO TCGA-E9-A5UP 
       46.59        39.09        38.37        41.72        25.81        26.40 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P4 TCGA-EW-A1P5 
       28.77        25.94        22.82        29.85        29.82        23.11 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 
       18.90        13.94        55.00        52.73        25.91        34.03 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD 
       17.52        23.51        15.22        16.77        24.99        33.21 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A441 
      109.87        79.10         2.60        11.57         7.10        32.75 
TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D6 TCGA-OL-A5RZ TCGA-OL-A66N 
        2.63        19.53        12.36        36.30        22.32        26.04 
TCGA-OL-A66P TCGA-PE-A5DC TCGA-S3-A6ZH 
       14.07        47.01        21.07 

$`9P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T 
       23.80        21.73        11.28        11.97        11.05        53.06 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       19.99        15.06        33.01        33.01        33.01        17.95 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR 
       50.24         2.56        19.20        98.33        17.23        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
        9.70        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       50.07        26.99        15.68        75.02        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       24.95        29.23        25.05        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK 
       13.94        11.41        52.96       108.07        48.46        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
      101.98        55.43       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       92.48       107.93        77.19         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       118.45        74.40        72.00        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY 
       24.72        63.29        99.19        54.64        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-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       32.55        25.28        50.47        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       48.46        31.73        23.47        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       52.47        17.19        18.15        10.59        36.23        39.65 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       91.07        29.98        56.28        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       24.39        21.30        23.21        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26J 
       34.29        35.47        33.11        20.19        29.56        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SD 
       11.34        10.59        10.29        13.41        14.70        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX 
       21.17        14.73        12.10        10.72         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A076 
        8.75        13.02         1.02        31.00        26.01        53.98 
TCGA-A8-A07F 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-A07Z TCGA-A8-A082 TCGA-A8-A085 
        8.98         7.99        24.99        45.07        18.05        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08T 
       13.02         0.99        38.01        28.96         9.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09D 
       43.00        40.01        30.97        41.98         9.99        50.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0AD TCGA-AC-A23C 
       15.02        14.01        12.00        13.02        38.04        19.23 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       22.95        73.91         5.72        22.26        73.05        40.57 
TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       86.66        60.92        87.12        26.04        74.14        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62Y 
       14.99        15.48        23.24        24.79        29.26        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-A04D TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        2.30         0.33         1.71         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        7.04         0.33         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M 
       12.33         0.30         0.33         0.33         5.33        61.35 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 
       81.63        95.70        68.75        69.83        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       50.86        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AR-A0TP 
       97.08        82.62        24.79        26.93        32.52       140.55 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AJ 
      109.02        98.93        64.83        65.36       107.21       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU 
      103.86        97.68        96.00        86.07        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
      118.59         2.76       104.28       105.27       102.84        98.76 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       89.00        85.64        93.83       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       143.38       281.29       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.52       146.50       112.37       233.62       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       81.17        78.02       263.28       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WY 
      282.90       169.51        97.48       188.68        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
        7.07        74.99       103.63        71.15        59.84        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.44        39.16        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 
       61.51        21.70        61.68        72.23        74.14        85.87 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE 
       77.75        74.14        41.75        46.39        81.73        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       67.10        38.01        78.28        15.65         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 
       44.81        81.83        31.00        63.32        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       53.26        24.56        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-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       35.93        20.12        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       37.55        66.05        51.16        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FB 
       12.00        55.69        49.58        25.81        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       122.83        33.99        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       55.00        53.98        28.14        26.14        38.60        83.31 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
       36.82        36.79        20.12       110.60        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M 
       23.51         9.63         5.26        18.87        21.76        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 
       11.77        12.66        12.66        48.53        12.56        12.59 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
       12.59        12.92        12.49        12.33        10.92        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26W TCGA-C8-A26X 
        0.16        12.03        12.95        12.33        12.53        12.36 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
       15.45        16.70         0.03         9.76        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.95        12.49        19.46        13.25        20.58        13.97 
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        55.50        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN 
       18.90        12.03        14.01        18.97        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        13.32        14.70        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        18.15        12.39        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU 
       14.50        19.92        17.69        55.30        15.85        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        43.04        15.32        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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       13.48         1.61        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        12.66        25.22        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-A14U TCGA-E2-A14V 
       47.15        40.96        38.24        33.17        43.33        34.26 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       69.34        63.62        23.24        19.43        21.04        23.87 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       25.05        22.82        17.29        18.21        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
        9.04        20.58        11.05        19.56        56.94        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 
       54.18        60.36        19.66        28.90        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
       34.82        32.88        36.82        22.29        34.16        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R3 
       41.62        35.77        25.84        18.94        28.27         2.56 
TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        3.02        45.01         1.12        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       42.25        37.74        41.03        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90        23.84        26.70         0.79        27.85        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-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        40.41        41.13        39.78        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        19.99         6.15        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 
       19.96        22.09        17.49        31.30         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM 
       11.84        21.24        13.28        10.62        17.06        15.32 
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-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 
       19.59        17.49        27.91        22.39         2.10        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        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        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       20.68        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        29.03        15.35        16.04       107.05 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           165.76            282.90 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           25.020            29.835 
[1] "0.0 - 165.8 (25.0)" "0.0 - 282.9 (29.8)"
[1] "hr=" "1.4"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED        21       15        0        2       104        64
  9P LOSS WILD-TYPE      68       68        6        4       248       189
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  9P LOSS MUTATED           1         55         15         19       10       5
  9P LOSS WILD-TYPE         1        100         12         46       10       8
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 21                68
  STAGE IA                15                68
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA              104               248
  STAGE IIB               64               189
  STAGE III                1                 1
  STAGE IIIA              55               100
  STAGE IIIB              15                12
  STAGE IIIC              19                46
  STAGE IV                10                10
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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    57 203  34  18
  9P LOSS WILD-TYPE 217 422 103  22
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              57               217
  T2             203               422
  T3              34               103
  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   141  92  51  24
  9P LOSS WILD-TYPE 365 266  68  53
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             141               365
  N1              92               266
  N2              51                68
  N3              24                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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   259  11
  9P LOSS WILD-TYPE 630  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    259   11
  9P LOSS WILD-TYPE  630   11
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             259               630
  1              11                11
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   306   7
  9P LOSS WILD-TYPE 761   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    306    7
  9P LOSS WILD-TYPE  761    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             306               761
  MALE                 7                 5
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   126 156
  9P LOSS WILD-TYPE 311 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    126  156
  9P LOSS WILD-TYPE  311  391
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              126               311
  YES             156               391
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P LOSS MUTATED                            0                           262
  9P LOSS WILD-TYPE                          1                           506
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P LOSS MUTATED                               25                   3
  9P LOSS WILD-TYPE                            176                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P LOSS MUTATED                       5                                9
  9P LOSS WILD-TYPE                     4                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  9P LOSS MUTATED                    3              6
  9P LOSS WILD-TYPE                 14             40
D58V9, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                262               506
  INFILTRATING LOBULAR CARCINOMA                25               176
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             3                14
  OTHER, SPECIFY                                 6                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"
D58V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0    22
  9P LOSS WILD-TYPE                                1    38
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          55   198
  9P LOSS WILD-TYPE                       126   546
D58V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         22                38
  BLACK OR AFRICAN AMERICAN                     55               126
  WHITE                                        198               546
[1] 4 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    13 245
  9P LOSS WILD-TYPE  26 629
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13  245
  9P LOSS WILD-TYPE   26  629
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  13                26
  NOT HISPANIC OR LATINO             245               629
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   237  40
  9Q LOSS WILD-TYPE 680 108
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              277               788 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               40               108 
$`9Q LOSS MUTATED`
TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A09C TCGA-A8-A09I TCGA-AO-A1KT 
       22.32        53.06        33.01         1.02        45.07        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL TCGA-EW-A1P3 TCGA-LL-A5YP 
        5.65         2.56        32.91        66.15        52.96        14.79 
TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
      133.05        13.68         7.96        28.01        18.02       101.98 
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-A0SX TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       50.43        20.75        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 
       35.93        26.96        21.90        35.31        37.45        35.67 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A4SB TCGA-A7-A4SD 
       29.79        31.73        25.15        23.74        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
       17.92        10.29        13.02         1.02        17.98        31.00 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08I 
        1.02         9.01        43.00        18.97         8.98        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A097 
       37.05        31.00        31.00         0.99        43.00        12.00 
TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 
       12.00        33.07        25.02        19.04        19.04        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH 
        0.99        27.02        17.03        99.35        90.71        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP 
       19.33        14.66        11.44        13.58         0.03        20.19 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM 
        0.33         0.33         0.23         1.78         7.36         0.16 
TCGA-AN-A0FJ TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW 
        7.96         0.36         0.33         0.33         0.33         5.59 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       80.28        66.77        81.63        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        60.56        61.87        82.62        11.51 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0TZ 
      130.09        15.62        98.33        84.10        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP 
       65.36       133.22       134.14       125.16       108.36        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R 
       99.32        86.53        33.73        50.89        99.78       112.77 
TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A2LK 
       97.84       105.30        98.66        99.62        93.30        54.21 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO 
       11.90       129.57       165.76       255.68        81.17       162.05 
TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A401 
      102.77        79.46        18.35        21.01        43.59        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B5 
       74.99        68.12        18.84        62.93        39.55        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BV 
       84.13        51.68        43.53        74.89        77.75        49.94 
TCGA-BH-A0C3 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ 
       89.06         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        25.08        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        55.50        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        12.16        13.51        12.46         0.16        12.36 
TCGA-C8-A26Z TCGA-C8-A27B TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 
       15.45        14.43        13.41        20.88        14.17        13.48 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 
       16.50        15.78        18.97        20.09        20.12        18.58 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XY 
       17.79        27.58        17.16        16.41        16.31        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O 
       14.14        16.04        10.09        12.26        46.59        44.68 
TCGA-E2-A14R TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       38.60        32.02        31.96        18.51        63.62        69.96 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A1AZ TCGA-E2-A1LB 
       25.05        23.34        20.71        21.63        76.57        75.81 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA 
      106.75       102.61         8.75        34.92        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 
       39.55         9.86        24.82         6.12        11.15        48.23 
TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22B TCGA-E9-A5UO TCGA-E9-A5UP 
       40.24        21.27        46.59        38.37        25.81        26.40 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A2FR 
       28.77        25.94        22.82        29.85        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        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DB 
       15.22        16.77        24.99        33.21       109.87        79.10 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7SZ 
        2.60        11.57        32.75        15.32         2.63        19.53 
TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZF 
       12.36        22.32        20.38        26.04        14.07        18.81 
TCGA-S3-A6ZH 
       21.07 

$`9Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        21.73        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E 
       19.99        15.06        33.01        33.01        17.95        49.05 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM 
       50.24        19.20        98.33        17.23        57.27        73.35 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
       10.42        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       50.07        26.99        15.68        75.02        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       24.95        29.23        25.05        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALI TCGA-3C-AALJ 
       13.94        11.41        52.96       108.07       131.67        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN 
       48.10        14.27        47.24        20.88        31.79        39.32 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19         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-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        74.40        72.00        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-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.90        32.55        25.28        50.47        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       19.33        48.46        31.73        23.47        22.45        20.25 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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-A3XW 
       10.59        36.23        39.65        91.07        29.98        56.28 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13E 
       21.14        34.29        35.47        30.61        33.11        20.19 
TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       29.56        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        14.93        21.17        14.73        12.10        10.72 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A075 
        9.37        10.42         8.75        13.02        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       53.98        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-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-A08L TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
        9.99       112.08        40.01        30.97        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W 
        9.99        50.04         1.02         8.98        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       14.01        12.00        13.02        38.04        19.23        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         5.72        22.26        73.05        40.57        86.66 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3EH 
       60.92        87.12        26.04        74.14        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
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-A049 TCGA-AN-A04A TCGA-AN-A04D 
        1.32         2.30         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.46         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         6.90         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         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03P 
        0.30         0.33         0.33         5.33        61.35        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J6 
       68.75        69.83        58.95        44.42        32.78        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 
       76.77        65.10        26.24        62.04        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      113.62       108.72       106.78       108.03       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       82.68        70.42        53.88        40.57        20.45        97.08 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT 
       24.79        26.93        32.52       140.55         5.26       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ 
       75.22        98.93        64.83        83.87       107.21       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU 
      103.86        97.68        96.00        86.07        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O 
       61.28        86.43       160.90        94.22       120.33       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
        2.76       104.28       105.27       102.84        50.96        98.76 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       89.00        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       86.53        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       38.96        10.59        77.62       143.38       281.29       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
      127.33        84.59       129.07       140.88        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      234.28        78.02       263.28       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ 
      282.90       169.51        97.48       188.68       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        58.55       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A40B 
       73.51       139.17       170.17        37.87         7.07       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        63.09        81.44 
TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ 
       39.16        37.22        32.02        18.21        61.51        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        85.87 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.95        74.14        41.75        46.39        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE 
       16.27        15.68        14.30        44.81        81.83        31.00 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB 
       63.32        15.16        63.39        53.26        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-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25        50.79         5.59        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        32.91         4.90        35.93        20.12 
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-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-A1F2 TCGA-BH-A1F6 
       55.69        49.58        17.69        25.81        31.53        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62       114.15       122.83        33.99        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O 
       53.98        28.14        26.14        38.60        83.31        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       36.79        20.12       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12N 
        9.63         5.26        18.87        21.76        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        48.53        12.56        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.92        12.49        12.33        10.92        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
       12.95        16.87        16.70         0.03         9.76        24.56 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y 
       33.99        12.95        13.02        12.49        19.46        56.81 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.25        20.58        13.97        19.20        14.17        17.49 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       55.50        18.15        18.90        12.03        53.00        14.01 
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-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       14.70        16.73        25.74        23.90        18.15        12.39 
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-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       55.30        15.85        16.64        12.99        15.16        43.04 
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-A27N 
       13.05        14.43        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.53        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        12.66        25.22        43.00        34.42        27.52 
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-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        33.17        75.98        43.33        34.26 
TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C 
       69.34        23.24        19.43        21.04        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 
       60.36        19.66        24.59        28.90        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1ND 
       34.82        32.88        36.82        22.29        34.16        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        35.24        25.84        18.94        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        45.01        32.09         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90        23.84        26.70         0.79        27.85        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-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 
       29.95        40.41        41.13        39.78        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-A2FW TCGA-EW-A6SC 
       10.52        14.43        34.55        19.96        22.09        31.30 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
        7.40        59.57       216.76        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 
       18.12        62.47        11.84        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
       10.62        17.06        14.70        14.47        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       15.68         7.46        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       36.36        28.87        24.72        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       41.92        42.77        17.36        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-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
        9.93        18.48        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26        17.03         3.81        66.84        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           255.68            282.90 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            25.91             28.93 
[1] "0.0 - 255.7 (25.9)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED        18       16        0        2        97        56
  9Q LOSS WILD-TYPE      71       67        6        4       255       197
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  9Q LOSS MUTATED           1         45         11         19        7       5
  9Q LOSS WILD-TYPE         1        110         16         46       13       8
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 18                71
  STAGE IA                16                67
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               97               255
  STAGE IIB               56               197
  STAGE III                1                 1
  STAGE IIIA              45               110
  STAGE IIIB              11                16
  STAGE IIIC              19                46
  STAGE IV                 7                13
  STAGE X                  5                 8
[1] 12  2
[1] TRUE
[1] "dimension of 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    53 174  34  17
  9Q LOSS WILD-TYPE 221 451 103  23
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              53               221
  T2             174               451
  T3              34               103
  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
  9Q LOSS MUTATED   133  80  39  23
  9Q LOSS WILD-TYPE 373 278  80  54
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             133               373
  N1              80               278
  N2              39                80
  N3              23                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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   232   8
  9Q LOSS WILD-TYPE 657  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    232    8
  9Q LOSS WILD-TYPE  657   14
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             232               657
  1               8                14
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   273   7
  9Q LOSS WILD-TYPE 794   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    273    7
  9Q LOSS WILD-TYPE  794    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             273               794
  MALE                 7                 5
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   105 144
  9Q LOSS WILD-TYPE 332 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    105  144
  9Q LOSS WILD-TYPE  332  403
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              105               332
  YES             144               403
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q LOSS MUTATED                            0                           232
  9Q LOSS WILD-TYPE                          1                           536
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q LOSS MUTATED                               22                   2
  9Q LOSS WILD-TYPE                            179                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q LOSS MUTATED                       4                                9
  9Q LOSS WILD-TYPE                     5                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  9Q LOSS MUTATED                    3              8
  9Q LOSS WILD-TYPE                 14             38
D59V9, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                232               536
  INFILTRATING LOBULAR CARCINOMA                22               179
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                21
  MUCINOUS CARCINOMA                             3                14
  OTHER, SPECIFY                                 8                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"
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                          57   173
  9Q LOSS WILD-TYPE                       124   571
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                     57               124
  WHITE                                        173               571
[1] 4 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    12 218
  9Q LOSS WILD-TYPE  27 656
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     12  218
  9Q LOSS WILD-TYPE   27  656
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                27
  NOT HISPANIC OR LATINO             218               656
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   142  31
  10P LOSS WILD-TYPE 775 117
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               173                892 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                31                117 
$`10P LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26E TCGA-A7-A2KD TCGA-A8-A084 TCGA-A8-A08F TCGA-AR-A2LR 
       19.20        31.36        22.32        15.06        33.01        57.27 
TCGA-E2-A1LG TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK 
       50.07       133.05       131.67         9.96        13.68        31.79 
TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       39.32        18.02        73.84        77.19        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1FX 
      107.93        67.33        25.22        18.21        17.36        60.72 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A13F 
        7.30        24.39        26.96        21.90        30.61        25.15 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A08I 
       13.74        21.17        17.98        53.98        14.01        12.00 
TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB 
        9.99        12.00        12.00         8.98        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH 
       38.04         5.72        33.04        19.33        14.66         6.48 
TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VC 
       29.26        14.96        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        60.56        26.93         5.26        75.22        83.87 
TCGA-AR-A1AN TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 
       96.00        94.22       104.28       112.77        50.96        89.00 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QQ TCGA-B6-A0IK 
       85.64        93.83        54.21        39.39        10.59        18.77 
TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 
       81.17       100.70       282.90        73.51       139.17        68.12 
TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT 
       62.93        39.55        84.13        37.22        21.70        77.75 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0EB TCGA-BH-A0EE 
       49.94        74.14        46.39        90.97        24.49        31.00 
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        35.93        51.16 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN 
       91.99        42.28        25.08        33.99        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        12.59        12.59 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
       12.49        11.28        12.03        12.33        20.25        12.53 
TCGA-C8-A26Y TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XB 
       12.95        14.17        18.90        53.00        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 
       75.98        18.51        21.63        56.94        14.07        22.19 
TCGA-E2-A1L7 TCGA-E2-A56Z TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 
       60.36         8.28        41.62        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        34.45        38.37        41.72 
TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
        1.94        23.84        26.70        23.11         7.86        18.90 
TCGA-EW-A6S9 TCGA-EW-A6SD TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A6FP TCGA-LL-A7T0 
       15.22        33.21        69.30         2.60        22.26        12.36 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG 
       36.36        23.47        86.96         0.16        18.48 

$`10P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E 
       11.28        11.97        11.05        53.06        29.03        19.99 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
       33.01        33.01        17.95         1.02        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       50.24        17.79         5.65         2.56        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       98.33        17.23        66.15        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 
       32.58        21.44        89.16         9.70        10.42        21.14 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-EW-A1J5 
       14.79        50.79        16.47        73.64        26.99        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 
       52.96        75.02        85.35        13.22        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       25.05        14.79        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
       11.41        52.96       108.07        48.46        47.61        11.44 
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-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       20.88         7.96        28.01        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        87.25       101.98        55.43       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX 
       24.79       114.81        92.48       107.93        98.99        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        33.76        61.58       101.72       134.40        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      118.45        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-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        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-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-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B 
       22.45        20.25        19.20        16.47        52.47        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        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        91.07        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       35.93        50.37        50.83        21.30        23.21        21.14 
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-A13H TCGA-A7-A26G TCGA-A7-A26J 
       29.79        31.73        20.19        29.56        23.74        20.61 
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-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       14.50        17.92        14.73        12.10        10.72        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-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-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        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-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-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       37.05        31.00        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       40.01        30.97        41.98         9.99         9.99        50.04 
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-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       19.23        22.95        73.91        22.26        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       74.14        32.45        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EH 
       25.05        14.99        15.48        23.24        24.79        16.80 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ 
       11.44        18.67         1.68         8.22        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-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.78         1.71         9.96         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS 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-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV 
        0.33         5.36        12.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        80.28        81.63        95.70        68.75        69.83 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       44.42        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04L 
       97.08        61.87        82.62        11.51        24.79       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
       15.62        32.52       140.55        98.33        84.10       109.02 
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       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        86.07        93.90        99.32        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        86.53        86.43        33.73       160.90        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
      120.33        99.78       118.59         2.76        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      102.84       105.30        98.76        98.66        99.62        93.30 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       71.05       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       40.54        33.30        38.96        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       11.90       275.87       129.57        50.70        65.52       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37       233.62       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       255.68        68.45       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       162.05       102.77       140.28        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       43.59       101.52       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       74.99        18.84       103.63        71.15        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 
       25.55        63.09        81.44        39.16        70.22        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        43.53        61.51        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW 
       72.23        75.48        74.14        76.60        85.87        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        89.06        81.73        77.98        67.10        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30         9.63        44.81        81.83        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        63.39        53.26        24.56        23.08 
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-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-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       42.35        44.81        32.91         4.90        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-A1ES TCGA-BH-A1ET 
       66.05         7.36        51.39        69.93       113.82        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-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48       120.62       114.15        33.17        74.73       122.83 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       63.35        55.00        53.98        55.50        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
      110.60        20.88        23.51         9.63         5.26        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-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
       12.56        12.16        13.51        12.92        12.46        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26X 
       10.92        11.34         0.16        12.95        12.33        12.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
       15.45        16.87        16.70         0.03         9.76        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        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        56.81        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        19.20        17.49        16.50        55.50 
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        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.64        12.99        43.04        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 
       48.03        16.41        13.48        17.06         1.61        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 
       12.66        25.22        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        69.34        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ 
        9.04        20.58        11.05        19.56        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       59.18         3.88        60.99        11.08        54.18        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       43.04        34.55        43.56        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       34.16        36.20        36.56        39.55        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       18.94        24.82        28.27        34.95         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE 
       11.15        48.23        45.01        32.09         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.03        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO 
       32.91        30.18        30.44        23.90         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
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-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-EW-A6SA 
       22.09        34.03        17.49        17.52        23.51        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        15.32        14.70        14.47         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68         7.46        19.53        19.59        17.49        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-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        18.81        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        17.39        17.26        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.03               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            282.90             281.29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            24.390             28.885 
[1] "0.0 - 282.9 (24.4)" "0.0 - 281.3 (28.9)"
[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        60        43
  10P LOSS WILD-TYPE      78       79        6        5       292       210
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1         32          6         13        3
  10P LOSS WILD-TYPE         1        123         21         52       17
                    vv
clus                 STAGE X
  10P LOSS MUTATED         1
  10P LOSS WILD-TYPE      12
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  4                 79
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                60                292
  STAGE IIB                43                210
  STAGE III                 1                  1
  STAGE IIIA               32                123
  STAGE IIIB                6                 21
  STAGE IIIC               13                 52
  STAGE IV                  3                 17
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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    27 116  22   9
  10P LOSS WILD-TYPE 247 509 115  31
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               27                247
  T2              116                509
  T3               22                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
  10P LOSS MUTATED    72  59  26  14
  10P LOSS WILD-TYPE 434 299  93  63
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               72                434
  N1               59                299
  N2               26                 93
  N3               14                 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   155   3
  10P LOSS WILD-TYPE 734  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    155    3
  10P LOSS WILD-TYPE  734   19
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              155                734
  1                3                 19
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   175   0
  10P LOSS WILD-TYPE 892  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    175    0
  10P LOSS WILD-TYPE  892   12
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              175                892
  MALE                  0                 12
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    68  87
  10P LOSS WILD-TYPE 369 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     68   87
  10P LOSS WILD-TYPE  369  460
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                68                369
  YES               87                460
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P LOSS MUTATED                            0                           131
  10P LOSS WILD-TYPE                          1                           637
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P LOSS MUTATED                               22                   0
  10P LOSS WILD-TYPE                            179                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P LOSS MUTATED                       6                                9
  10P LOSS WILD-TYPE                     3                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  10P LOSS MUTATED                    1              5
  10P LOSS WILD-TYPE                 16             41
D60V9, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 131                637
  INFILTRATING LOBULAR CARCINOMA                 22                179
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  5                 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"
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                          25   120
  10P LOSS WILD-TYPE                       156   624
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                      25                156
  WHITE                                         120                624
[1] 4 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     4 139
  10P LOSS WILD-TYPE  35 735
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  139
  10P LOSS WILD-TYPE   35  735
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              139                735
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   191  39
  10Q LOSS WILD-TYPE 726 109
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               230                835 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                39                109 
$`10Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26E TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A084 TCGA-A8-A08F 
       19.20        31.36        22.32        29.03        15.06        33.01 
TCGA-A8-A09E TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A2LR TCGA-E2-A1LG 
       49.05        32.91        19.20        66.15        57.27        50.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
      133.05       131.67         9.96        13.68        31.79        39.32 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       18.02        73.84        77.19        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 
       91.07         7.30        24.39        26.96        21.90        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        31.73        25.15        13.74        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A07R 
       14.73        10.29        17.98        53.98        14.01         8.98 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09R 
       12.00         9.99        43.00        12.00        12.00         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        19.23         5.72        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IW 
       19.33        14.66         6.48        14.96        17.42        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW 
        0.03         1.12         7.36         0.33         0.33         0.36 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.30         0.33         0.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A124 
       66.77        58.95        44.42        21.53        72.00       115.27 
TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 
       60.56        26.93         5.26        75.22        98.93        83.87 
TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W 
       99.32        33.73        94.22       104.28       112.77        50.96 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QQ 
       89.00        85.64        93.83        54.21        39.39        10.59 
TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI 
       18.77       255.68        81.17       100.70       282.90        73.51 
TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B3 
      139.17        74.99        68.12        62.93        59.84        39.55 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       84.13        37.22        21.70        77.75        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 
       74.14        46.39        24.49        31.00        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        35.93         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        25.08       114.15        33.99 
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        12.59        12.59        12.49        11.28 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        12.33        12.95        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 
       12.95        24.56        56.81        13.97        14.17        17.49 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ 
       53.00        20.12        18.58        18.15        15.22        21.83 
TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27T 
       16.41        12.99        15.16        16.04        14.43        13.08 
TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A159 TCGA-E2-A15F 
       40.11        47.15        75.98        18.51        25.05        21.63 
TCGA-E2-A15P TCGA-E2-A1IE TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LK 
       19.56        77.65        22.19        60.36       106.75         8.75 
TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 
        8.28        38.76        41.62        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        34.45        38.37        41.72 
TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1OW TCGA-EW-A1OZ 
        1.94        29.72        23.84        26.70        22.82        40.41 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A2FV TCGA-EW-A6S9 TCGA-EW-A6SD 
       23.11         7.86        18.90        25.91        15.22        33.21 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FP 
       69.30         2.60        11.84        11.57         7.10        22.26 
TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX 
       19.59        36.36        23.47        28.21        86.96         0.16 
TCGA-S3-A6ZG TCGA-S3-A6ZH 
       18.48        21.07 

$`10Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        24.26        23.80        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A08S 
       11.28        11.97        11.05        53.06        19.99        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01        17.95         1.02        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT 
       19.79        14.53        19.33        13.71        50.24        17.79 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A5QM TCGA-BH-A0B6 
        5.65         2.56        98.33        17.23        73.35        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A2P5 
       21.14        14.79        50.79        16.47        73.64        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       29.23        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK 
       13.94        11.41        52.96       108.07        48.46        47.61 
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       11.44         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        20.88         7.96        28.01        18.21       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       78.41       121.94        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CV 
       99.12        24.79       114.81        92.48       107.93        98.99 
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-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       118.45        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-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        44.88        50.43        44.28        17.13         8.38 
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-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 
       23.77        23.47        22.45        20.25        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        36.23        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        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CE 
       50.37        50.83        21.30        23.21        21.14        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-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.56        23.74        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.41        14.70        14.93        17.92        12.10        10.72 
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-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-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        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-A085 
        7.99        24.99         9.99        45.07        18.05        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-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
       31.00        31.00         0.99       112.08        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
       41.98         9.99         9.99        50.04        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       25.02        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G 
       19.04        13.02         0.99        27.02        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN 
       60.92        87.12        26.04        74.14        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IV 
       23.24        24.79        29.26        16.80        11.44        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         7.46         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         6.90         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 
        5.36        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        69.83        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-A0JJ 
       50.70        50.86        76.77        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        82.68        70.42        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       20.45        97.08        61.87        82.62        11.51        24.79 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
      130.09        15.62        32.52       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
      109.02        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M 
       61.28        86.53        86.43       160.90        50.89       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59         2.76        97.84       105.27       102.84 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.30        98.76        98.66        99.62        93.30        71.05 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
      166.42        20.25        86.53        63.62        38.17        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       33.30        38.96        77.62       143.38       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.52       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      233.62       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.28        89.46       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.46        18.35        21.01       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.55        43.59       101.52 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A409 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
       71.15        20.45        25.55        63.09        81.44        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       70.22        51.68        32.02        18.21        43.53        61.51 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       85.87        41.75        89.06        90.97        81.73        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       67.10        38.01        29.98        13.91        78.28        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        79.00        67.86        70.88        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        81.83 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       24.56        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-A18F TCGA-BH-A18G TCGA-BH-A18J 
       24.95        42.35        44.81        32.91         4.90        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-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05        51.39        69.93       113.82        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-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62        33.17        74.73       122.83        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       53.98        55.50        28.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 
       12.66        48.53        12.56        12.16        13.51        12.92 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HO 
       12.46        12.33        10.92        11.34         0.16        12.33 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       15.45        16.87        16.70         0.03         9.76        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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-A147 
       20.88        13.25        20.58        14.17        13.48        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        55.50        15.78        18.15        18.90        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-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        43.04        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-A27K 
       14.24        14.14        17.42        13.45        13.05        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       23.87        23.34        22.82        17.29        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       56.94        14.07        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG 
       33.01        32.35        28.50        37.25        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       33.73        33.70        28.44        59.18         3.88        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        19.66        24.59        75.81        28.90 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      102.61        43.04        34.55        43.56        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       34.16        36.20        36.56        39.55        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       18.94        24.82        28.27        34.95         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE 
       11.15        48.23        45.01        32.09         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.03        40.73        40.50        20.12         0.69        38.99 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        7.13        24.56        12.33         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        30.44        23.90         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        28.77        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       41.13        39.78        29.82        18.48        30.08        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        17.52 
TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 
       23.51        16.77        24.99        31.30         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       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-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       62.47        21.24        13.28        10.62        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       15.32        14.70        14.47         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        19.53        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        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-A8LY TCGA-PL-A8LZ 
       40.11         8.91        47.01        64.21         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       18.81        20.68        19.27        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.03               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            282.90             281.29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.44              29.26 
[1] "0.0 - 282.9 (24.4)" "0.0 - 281.3 (29.3)"
[1] "hr=" "1.6"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED        17        9        1        1        75        54
  10Q LOSS WILD-TYPE      72       74        5        5       277       199
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1         38          7         21        4
  10Q LOSS WILD-TYPE         1        117         20         44       16
                    vv
clus                 STAGE X
  10Q LOSS MUTATED         2
  10Q LOSS WILD-TYPE      11
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                  9                 74
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                75                277
  STAGE IIB                54                199
  STAGE III                 1                  1
  STAGE IIIA               38                117
  STAGE IIIB                7                 20
  STAGE IIIC               21                 44
  STAGE IV                  4                 16
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    40 148  28  13
  10Q LOSS WILD-TYPE 234 477 109  27
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               40                234
  T2              148                477
  T3               28                109
  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   100  73  32  22
  10Q LOSS WILD-TYPE 406 285  87  55
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0              100                406
  N1               73                285
  N2               32                 87
  N3               22                 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   201   4
  10Q LOSS WILD-TYPE 688  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    201    4
  10Q LOSS WILD-TYPE  688   18
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              201                688
  1                4                 18
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   230   1
  10Q LOSS WILD-TYPE 837  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    230    1
  10Q LOSS WILD-TYPE  837   11
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              230                837
  MALE                  1                 11
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    92 116
  10Q LOSS WILD-TYPE 345 431
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     92  116
  10Q LOSS WILD-TYPE  345  431
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                92                345
  YES              116                431
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q LOSS MUTATED                            0                           180
  10Q LOSS WILD-TYPE                          1                           588
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q LOSS MUTATED                               25                   1
  10Q LOSS WILD-TYPE                            176                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q LOSS MUTATED                       6                                9
  10Q LOSS WILD-TYPE                     3                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  10Q LOSS MUTATED                    1              8
  10Q LOSS WILD-TYPE                 16             38
D61V9, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 180                588
  INFILTRATING LOBULAR CARCINOMA                 25                176
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  8                 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"
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0    19
  10Q LOSS WILD-TYPE                                1    41
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          46   145
  10Q LOSS WILD-TYPE                       135   599
D61V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          19                 41
  BLACK OR AFRICAN AMERICAN                      46                135
  WHITE                                         145                599
[1] 4 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     4 189
  10Q LOSS WILD-TYPE  35 685
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  189
  10Q LOSS WILD-TYPE   35  685
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              189                685
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   227  41
  11P LOSS WILD-TYPE 690 107
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               268                797 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                107 
$`11P LOSS MUTATED`
TCGA-A7-A26E TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 TCGA-A8-A09E 
       31.36        53.06        33.01        33.01        17.95        49.05 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A2LL 
       45.07        16.57        17.79         2.56        32.91        66.15 
TCGA-BH-A0B6 TCGA-BH-A18H TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1L8 TCGA-GM-A2DO 
       81.63        21.44        10.42        14.79        73.64        85.35 
TCGA-LL-A5YP TCGA-Z7-A8R5 TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T 
       14.79       108.07        13.68        39.32        18.02        73.84 
TCGA-A2-A0CO TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET 
      114.81        56.81        34.55        79.76        74.40        35.05 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX 
       50.43        17.13        21.90        18.61        23.77        60.72 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A7-A0CE 
       42.44       105.34        33.93        47.31        50.83        35.31 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A4SA TCGA-A7-A4SE 
       35.67        31.73        20.19        25.15        14.93        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       14.73        10.29        13.02         1.02         9.01        43.00 
TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
       14.01         9.99        18.05        19.96        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09T 
       31.00         0.99        43.00        12.00        12.00        19.04 
TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG 
       19.04        17.03        22.95        73.05        99.35        60.92 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A6IX 
       26.04        33.04        16.80        14.96        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         7.46         6.90 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M 
        7.04         0.36         0.33         0.33         0.33        61.35 
TCGA-AO-A03P TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JL 
       95.70        20.32        53.03        21.53        50.70        55.33 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ 
       70.42        60.56        53.88       109.02        75.22       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK 
       65.36        83.87       134.14       107.21       108.36       103.86 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24Z 
       94.29        86.53       160.90       112.77       105.27        98.66 
TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IO 
       39.39        11.90        65.52       146.50        18.77       165.76 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      282.90        79.46        18.35        21.01       245.10       101.52 
TCGA-B6-A1KN TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AV 
      139.17         7.07        74.99        18.84       103.63        59.84 
TCGA-BH-A0AY TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP 
       25.55        70.22        37.22        18.21        74.89        75.48 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DI TCGA-BH-A0DK 
       49.94        41.75        46.39        89.06        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HX 
       78.28        31.00        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-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A203 
      113.82        17.69        31.53        25.08       114.15        38.60 
TCGA-BH-A28Q TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q 
       36.79        10.52        11.93        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66        12.66        12.59        12.92        12.49        10.92 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 
       11.28        12.03        12.95        12.36        12.95         9.76 
TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 
       12.49        56.81        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        43.04        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-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15P 
       31.96        18.51        25.05        20.71        18.21        19.56 
TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH 
       37.25        70.36        33.73        60.36        24.59       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N9 
      102.61         8.75        43.04        34.92        17.69        36.20 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1RF TCGA-E9-A1RG 
       36.56        41.62        35.24        18.94         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       46.59        47.64        42.25        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OZ 
       40.73        38.07        30.18        25.81        26.40        40.41 
TCGA-EW-A1P4 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A6S9 TCGA-EW-A6SA 
       29.82         6.15        14.43        55.00        15.22        16.77 
TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP 
       85.15        69.30         7.10        15.32        14.47        22.26 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5RW TCGA-OL-A5RZ 
       12.36        19.59        27.91        36.30        36.36        22.32 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
       65.62        41.92        17.36         0.16        18.81        18.48 
TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-XX-A89A TCGA-Z7-A8R6 
       21.07        17.03        16.04       107.05 

$`11P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        38.30        23.61        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       21.73        22.32        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09K TCGA-AC-A3W6 
       19.99        15.06        33.01         1.02        29.98        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A7U7 
       14.53        19.33        13.71        50.24         5.65        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA 
       98.33        17.23        57.27        73.35        54.05        32.58 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1LG 
       89.16         9.70        21.14        50.79        16.47        50.07 
TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LD-A74U TCGA-LL-A440 
       26.99        15.68        52.96        75.02        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       29.23        25.05        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK 
       11.41        52.96       133.05       131.67        48.46        47.61 
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       11.44         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-A0SO 
       14.27        47.24        20.88        31.79         7.96        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W 
       18.21       143.15        78.41       121.94        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CR 
       55.43       136.73        99.12        24.79        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        67.33 
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-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        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-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52         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-A0YH 
       20.75        32.55        25.28        18.21        50.47        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-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C 
       22.45        20.25        19.20        16.47        52.47        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       18.15        10.59        36.23        39.65        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        56.28        35.93        50.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG 
       21.30        23.21        26.96        21.14        21.90        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13H 
       35.47        30.61        37.45        33.11        29.79        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        13.74        14.50        17.92        12.10        10.72 
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-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07G 
       31.00        26.01        17.03        53.98        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-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       24.99        45.07        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
       28.96        12.00        31.00       112.08        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
       41.98         9.99         9.99        50.04        33.07         1.02 
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-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        27.02        38.04        19.23 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       73.91         5.72        22.26        40.57        86.66        90.71 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       87.12        74.14        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62V TCGA-AC-A62Y 
       15.48        23.24        24.79        29.26        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       18.67         1.68         8.22        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-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         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-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.30         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        69.83        58.95        44.42 
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-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       50.86        72.00        76.77        65.10        26.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
      102.31        98.27        82.68        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       15.62        32.52       140.55        98.33         5.26        84.10 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AJ 
       98.93        64.83        55.86       133.22       125.16       101.00 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.43        33.73        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U 
       99.78       118.59         2.76       104.28        97.84       102.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
      105.30        50.96        98.76        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       54.21        63.62        38.17        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38       281.29       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       50.70       112.37       233.62       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.28       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ 
       89.46       169.51        97.48       188.68       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      129.70        28.27        68.94        58.55        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        37.87        85.35        68.12        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 
       20.45        63.09        81.44        39.55        39.16        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       51.68        32.02        43.53        61.51        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       72.23        74.14        76.60        85.87        77.75        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       74.14        90.97        81.73        77.98        67.10        38.01 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       81.83        24.49        63.32        30.35        10.78        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       53.26        24.56        41.00        26.50        20.38         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        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        20.12        90.84        72.56        37.74 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55        66.05        51.39        51.16        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 
       42.28        12.00        55.69        49.58        25.81        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       122.83        33.99        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        53.98        55.50        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        36.82        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      110.60        20.88        18.64        23.51         9.63         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V 
       18.87        21.76         9.44        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        48.53        12.56        12.16        13.51        12.59 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HO 
       12.46        12.33        11.34         0.16        12.33        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       20.25        12.53        15.45        16.87        16.70         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR 
       24.56        14.43        33.99        12.95        13.02        13.41 
TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J9 
       19.46        13.25        20.58        14.17        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       16.50        55.50        12.03        53.00        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        55.30        16.41        15.85        16.64 
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        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       13.48        17.06         1.61        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        12.66        25.22        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        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       34.26        32.02        69.34        63.62        69.96        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        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       11.05        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF 
       87.22        33.01        32.35        28.50        77.65        37.41 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A2P6 
       11.08        54.18        19.66        75.81        28.90        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 
       43.56         8.28        30.61        38.76        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NE 
       32.88        36.82        22.29        34.16        39.55        35.77 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        24.82        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        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
       40.24         1.12        46.65        34.45        32.05        37.74 
TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       39.09        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        7.13        24.56        12.33        29.72         9.47        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE 
       30.44        23.90        23.84        26.70         0.79        27.85 
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-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       41.13        39.78        23.11        18.48        30.08         7.86 
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        17.52 
TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       23.51        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
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-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-A7W6 TCGA-LD-A9QF 
       62.47        11.84        11.57        21.24        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       32.75        17.06        14.70         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 
        7.46        19.53        17.49        22.39         2.10        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       31.99        58.62        34.92        28.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO 
       26.70        23.47        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-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
        0.26         9.93        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 
       17.26         3.81        66.84        29.03        15.35 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.03               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            282.90             281.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            26.955             28.270 
[1] "0.0 - 282.9 (27.0)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        20       13        1        1        85        61
  11P LOSS WILD-TYPE      69       70        5        5       267       192
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         51         14         17        4
  11P LOSS WILD-TYPE         2        104         13         48       16
                    vv
clus                 STAGE X
  11P LOSS MUTATED         2
  11P LOSS WILD-TYPE      11
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 13                 70
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                85                267
  STAGE IIB                61                192
  STAGE III                 0                  2
  STAGE IIIA               51                104
  STAGE IIIB               14                 13
  STAGE IIIC               17                 48
  STAGE IV                  4                 16
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    59 159  34  18
  11P LOSS WILD-TYPE 215 466 103  22
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               59                215
  T2              159                466
  T3               34                103
  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   118  86  42  19
  11P LOSS WILD-TYPE 388 272  77  58
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              118                388
  N1               86                272
  N2               42                 77
  N3               19                 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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   224   6
  11P LOSS WILD-TYPE 665  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    224    6
  11P LOSS WILD-TYPE  665   16
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              224                665
  1                6                 16
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   267   3
  11P LOSS WILD-TYPE 800   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    267    3
  11P LOSS WILD-TYPE  800    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE              267                800
  MALE                  3                  9
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   121 130
  11P LOSS WILD-TYPE 316 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    121  130
  11P LOSS WILD-TYPE  316  417
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               121                316
  YES              130                417
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P LOSS MUTATED                            0                           206
  11P LOSS WILD-TYPE                          1                           562
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P LOSS MUTATED                               35                   5
  11P LOSS WILD-TYPE                            166                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P LOSS MUTATED                       2                               10
  11P LOSS WILD-TYPE                     7                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  11P LOSS MUTATED                    3              9
  11P LOSS WILD-TYPE                 14             37
D62V9, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 206                562
  INFILTRATING LOBULAR CARCINOMA                 35                166
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              3                 14
  OTHER, SPECIFY                                  9                 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"
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1    18
  11P LOSS WILD-TYPE                                0    42
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          62   162
  11P LOSS WILD-TYPE                       119   582
D62V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          18                 42
  BLACK OR AFRICAN AMERICAN                      62                119
  WHITE                                         162                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"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4 216
  11P LOSS WILD-TYPE  35 658
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4  216
  11P LOSS WILD-TYPE   35  658
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              216                658
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   317  45
  11Q LOSS WILD-TYPE 600 103
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               362                703 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                45                103 
$`11Q LOSS MUTATED`
TCGA-A2-A04V TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S 
       63.12        31.36        11.28        53.06        33.01        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       33.01        17.95        49.05        45.07        29.98        16.57 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A2LL TCGA-BH-A18H 
       17.79         2.56        32.91        98.33        66.15        21.44 
TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1L8 TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LL-A5YP 
       10.42        14.79        73.64        15.68        85.35        14.79 
TCGA-S3-AA17 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALK TCGA-A1-A0SD TCGA-A1-A0SE 
       13.94       108.07       133.05        47.61        14.37        43.43 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R 
       13.68         7.96        39.32        18.21        18.02       121.94 
TCGA-A2-A04T TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX 
       73.84       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        36.23        39.65        33.93        47.31 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC 
       50.83         7.30        35.31        30.61        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A4SA TCGA-A7-A4SB 
       31.73        20.19        25.15        29.56        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Z 
       14.50        21.17        14.73        10.29        13.02         1.02 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08G 
        9.01        43.00        14.01         9.99        18.05        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A097 
       37.05         9.99        31.00        31.00        43.00        12.00 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A2 
       12.00        50.04        33.07         8.98        19.04        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        27.02        17.03        19.23        22.95 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3HN 
       73.05        99.35        60.92        26.04        33.04        16.31 
TCGA-AC-A3QQ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.13        29.26        14.96        18.67        13.58        12.26 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AJ 
        0.03         1.12         0.33         0.23         2.96         9.96 
TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.46         6.90         7.04         0.36         0.33         5.36 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P 
        0.33         0.33         5.59        80.28        61.35        95.70 
TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JG 
       69.83        21.40        20.32        53.03        21.53        26.24 
TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AR-A0TT 
       55.33        70.42        60.56        11.51        15.62       109.02 
TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       75.22       107.24        65.36       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
      107.21       108.36       103.86        94.29        61.28        86.53 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
      160.90        94.22       112.77        98.66        89.00        71.05 
TCGA-AR-A2LK TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IK 
       54.21        39.39        11.90       129.57       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW 
      127.33        68.45        81.17       282.90        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A400 
       21.01       245.10        58.55       101.52       139.17         7.07 
TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
       74.99        18.84       103.63        62.93        25.55        63.09 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BV 
       70.22        37.22        18.21        74.89        75.48        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DK 
       41.75        46.39        89.06        81.73        77.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 
       78.28        14.30        31.00        63.32        15.16        23.08 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
       52.96        26.50        13.61        12.89        27.25        50.79 
TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EY 
       23.05        26.66        30.28        69.93       113.82        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12M 
       31.53        25.08        36.79        10.52        18.64        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A132 
       11.77        12.66        12.66        12.66        48.53        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
       12.92        12.49        10.92        11.34        11.28        12.03 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 
       12.95        12.53        12.36        12.95        15.45         9.76 
TCGA-C8-A27A TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 
       24.56        12.49        56.81        20.88        13.97        13.48 
TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK 
       14.17        15.78        18.15        18.90        18.97        20.12 
TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU 
       17.79        25.74        23.90        15.22        16.31        12.99 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27R TCGA-D8-A27V 
       15.32        15.52        13.45        14.43        10.09        12.53 
TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S 
       12.26        43.00        46.59        44.68        38.60        33.17 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       34.26        31.96        21.04        25.05        20.71        18.21 
TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH 
        9.04        11.05        19.56        37.25        70.36        33.73 
TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z 
       11.08        60.36        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        17.69        36.82        36.20        36.56 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A1RG 
       18.94        24.82        34.95        48.23         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A247 
       47.64        38.37        41.03        41.72        40.73        38.99 
TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW 
       12.33        38.07        30.18        25.81        26.40        12.20 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P4 
       18.90        13.25        16.57        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        17.52 
TCGA-EW-A424 TCGA-EW-A6SA TCGA-GM-A2D9 TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LD-A7W6 
       23.51        16.77        59.57        69.30         7.10        13.28 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
       15.32        14.47        22.26        16.08        19.53        12.36 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RY 
       19.59        27.91         2.10        58.62        36.36        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-OL-A66P 
       22.32        20.38        65.62        41.92        17.36        14.07 
TCGA-OL-A6VO TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       28.21        47.01         0.16        18.81        18.48        21.07 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

$`11Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        19.20        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 
       22.32        11.97        11.05        29.03        19.99        15.06 
TCGA-A8-A09C TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
        1.02        19.79        14.53        19.33        13.71        50.24 
TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AR TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 
        5.65        19.20        17.23        57.27        73.35        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O 
       54.05        32.58        89.16         9.70        21.14        50.79 
TCGA-E2-A1BC TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LD-A74U 
       16.47        50.07        26.99        52.96        75.02        13.22 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       24.95        29.23        25.05        14.50        40.08        18.87 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AALI TCGA-3C-AALJ TCGA-4H-AAAK TCGA-5T-A9QA 
       11.41        52.96       131.67        48.46        11.44         9.96 
TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
        8.52        48.10        14.27        47.24        20.88        31.79 
TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       28.01       143.15        78.41        87.25       101.98        55.43 
TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       99.12        92.48       107.93        77.19         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM 
      107.93        67.33        34.55        33.76        61.58       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV 
      134.40        80.28       118.45        72.00        34.29        31.82 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       24.72        63.29        99.19        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YE 
       17.52         8.38        17.46        18.90        25.28        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       21.90        21.67        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-A25C 
       22.45        20.25        19.20        16.47        52.47        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       18.15        10.59        91.07        29.98        32.75        56.28 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       35.93        50.37        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.14        21.90        34.29        35.47        37.45        33.11 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX 
       14.70        17.92        12.10        10.72         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       17.03        53.98        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I 
       36.95        13.02         0.99        38.01        28.96        12.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
        0.99       112.08        40.01        30.97        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        9.99         1.02        25.02        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       12.00         0.99        38.04        73.91         5.72        22.26 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        86.66        90.71        87.12        74.14        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM 
       14.66        32.45         6.48        14.83        22.19        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EH TCGA-AC-A62V 
       14.99        15.48        23.24        24.79        16.80        11.44 
TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       17.42         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.33         0.62         1.78         1.71         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-A0FV TCGA-AN-A0FX 
        7.96         7.00         7.59         7.17         0.33         0.33 
TCGA-AN-A0FY 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-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V 
        5.33        66.77        81.63        68.75        58.95        44.42 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JB 
       32.78        52.18        26.04        37.48        22.36        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A0JM 
       50.86        72.00        76.77        65.10        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        82.68        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 
       61.87        82.62        24.79        26.93       130.09        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX 
      140.55        98.33         5.26        84.10        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO 
       55.86       125.16       101.00        97.68        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       93.90        99.32        37.81        86.43        33.73        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
      105.27       102.84       105.30        50.96        98.76        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        93.83       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       63.62        38.17        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       143.38       281.29       275.87        50.70        65.52 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       233.62        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      255.68       212.25       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.28       100.70        89.46       169.51        97.48 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
      188.68       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A408 
       43.59        73.51       170.17        37.87        85.35        68.12 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       71.15        59.84        20.45        81.44        39.55        39.16 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       84.13        51.68        32.02        43.53        61.51        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        72.23        74.14        76.60        85.87        77.75 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       77.95        74.14        90.97        67.10        38.01        29.98 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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        81.83 
TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        30.35        10.78        63.39        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW 
       41.00        20.38         5.85         2.50        36.85        51.32 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
        5.59        23.93        24.95        42.35        44.81        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        20.12        90.84        72.56        37.74 
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-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-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        97.48       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 
      122.83        33.99        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
       57.83       130.16        36.82        20.12       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ 
       12.16        13.51        12.59        12.46        12.33         0.16 
TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.33        12.33        20.25        16.87        16.70         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        33.99        12.95        13.02        13.41        19.46 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        20.58        14.17        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JL 
       55.50        12.03        53.00        14.01        20.09        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-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        27.58        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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.41        15.85        16.64        15.16        43.04        16.54 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H 
        9.93        14.24        14.14        17.42        16.04        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       48.03        16.41        13.48        17.06         1.61        13.08 
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        12.66        25.22 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14T TCGA-E2-A14U 
       28.87        47.15        40.96        38.24        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       19.43        23.87        23.34        22.82        17.29        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S 
       12.92        55.63        53.92        20.58        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       28.50        77.65        37.41        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
        3.88        22.19        60.99        54.18        19.66        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       28.90       106.75       102.61        34.55        43.56        30.61 
TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
       38.76        34.82        32.88        22.29        34.16        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 
       41.62        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        11.15        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         1.12        46.65        46.59        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       42.25        37.74        39.09        40.50        20.12         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         9.47        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE 
       30.44        23.90        23.84        26.70         0.79        27.85 
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-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        41.13        39.78        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH 
        7.86        18.90        19.99        10.52        34.55        19.96 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-EW-A6SB 
       25.91        22.09        34.03        17.49        15.22        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30        33.21         7.40       109.87       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-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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN 
       11.57        21.24        10.62        32.75        17.06        14.70 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5D6 
        2.63        15.68         7.46        17.49        22.39        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I 
       58.52        31.99        34.92        28.87        26.70        23.47 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD 
       42.77        26.04        19.73        40.11         8.91        64.21 
TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
       86.96         0.26         9.93        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       17.39        17.26        17.03         3.81        66.84        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 
            282.90             281.29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            25.115             29.720 
[1] "0.0 - 282.9 (25.1)" "0.0 - 281.3 (29.7)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        22       25        2        2       113        90
  11Q LOSS WILD-TYPE      67       58        4        4       239       163
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           1         65         14         20        6
  11Q LOSS WILD-TYPE         1         90         13         45       14
                    vv
clus                 STAGE X
  11Q LOSS MUTATED         4
  11Q LOSS WILD-TYPE       9
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  22                 67
  STAGE IA                 25                 58
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA               113                239
  STAGE IIB                90                163
  STAGE III                 1                  1
  STAGE IIIA               65                 90
  STAGE IIIB               14                 13
  STAGE IIIC               20                 45
  STAGE IV                  6                 14
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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    82 219  46  18
  11Q LOSS WILD-TYPE 192 406  91  22
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               82                192
  T2              219                406
  T3               46                 91
  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   163 118  54  24
  11Q LOSS WILD-TYPE 343 240  65  53
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0              163                343
  N1              118                240
  N2               54                 65
  N3               24                 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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   292   8
  11Q LOSS WILD-TYPE 597  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    292    8
  11Q LOSS WILD-TYPE  597   14
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              292                597
  1                8                 14
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   359   7
  11Q LOSS WILD-TYPE 708   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    359    7
  11Q LOSS WILD-TYPE  708    5
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE              359                708
  MALE                  7                  5
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   161 183
  11Q LOSS WILD-TYPE 276 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    161  183
  11Q LOSS WILD-TYPE  276  364
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               161                276
  YES              183                364
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q LOSS MUTATED                            0                           264
  11Q LOSS WILD-TYPE                          1                           504
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q LOSS MUTATED                               69                   4
  11Q LOSS WILD-TYPE                            132                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q LOSS MUTATED                       2                               11
  11Q LOSS WILD-TYPE                     7                               19
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  11Q LOSS MUTATED                    4             11
  11Q LOSS WILD-TYPE                 13             35
D63V9, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 264                504
  INFILTRATING LOBULAR CARCINOMA                 69                132
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 19
  MUCINOUS CARCINOMA                              4                 13
  OTHER, SPECIFY                                 11                 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"
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                          77   227
  11Q LOSS WILD-TYPE                       104   517
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                      77                104
  WHITE                                         227                517
[1] 4 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    12 286
  11Q LOSS WILD-TYPE  27 588
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  286
  11Q LOSS WILD-TYPE   27  588
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              286                588
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED   124  25
  12P LOSS WILD-TYPE 793 123
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               149                916 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                123 
$`12P LOSS MUTATED`
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A09I TCGA-AR-A1AR 
       21.73        22.32        53.06        33.01        45.07        17.23 
TCGA-AR-A2LL TCGA-BH-A18H TCGA-LL-A5YP TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A0D1 
       66.15        21.44        14.79        20.88        13.68        34.55 
TCGA-A2-A0T0 TCGA-A2-A0YF TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A3XT 
       17.52        50.47        52.47        42.44        17.19        91.07 
TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA 
       47.31        50.83        24.39        26.96        30.61        35.67 
TCGA-A7-A13D TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A07G 
       31.73        14.93        17.92        10.29        17.98        18.97 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A09Q TCGA-AC-A23H TCGA-AC-A2QI 
        0.99        43.00        40.01        25.02         5.72        19.33 
TCGA-AC-A2QJ TCGA-AC-A3W7 TCGA-AC-A6IV TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AN-A0AM 
       14.66        15.48        18.67         8.22         1.12         0.16 
TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        6.44         7.00         7.59         0.33         0.33        12.33 
TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A0J4 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL 
       81.63        69.83        52.18        50.70        72.00        55.33 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A1AI 
      108.03        82.68         5.26       107.24        65.36       108.36 
TCGA-AR-A1AJ TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
      101.00        50.89       120.33        99.62        93.30        85.64 
TCGA-AR-A256 TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RE 
       93.83       146.50       112.37       233.62        18.77       255.68 
TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A1KF TCGA-B6-A1KN 
      234.28       102.77       282.90       169.51       101.52       139.17 
TCGA-B6-A409 TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BW TCGA-BH-A0C0 
       18.84        39.55        84.13        75.48        77.95        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EE 
       46.39        90.97        67.10         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        55.50        57.83 
TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A26Y TCGA-C8-A27A 
       12.66        13.51        12.59        12.59        12.95        24.56 
TCGA-D8-A142 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1X5 TCGA-D8-A1XK TCGA-D8-A1XM 
       13.97        18.90        53.00        18.58        14.50        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A14Q TCGA-E2-A14Z 
       16.41        16.64        16.04        40.41        38.24        18.51 
TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1B5 TCGA-E2-A1BD 
       63.62        21.04        25.05        20.71        32.35        37.25 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       60.99        60.36        24.59       106.75       102.61         8.75 
TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1NH TCGA-E9-A1R4 TCGA-E9-A22G TCGA-E9-A3X8 
       34.92        17.69        18.94         6.12        40.73        30.44 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A3U0 
       25.81        26.40        29.85         6.15        13.94        17.49 
TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A6FR 
       16.77        31.30        33.21        86.96        15.32        16.08 
TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66K TCGA-UU-A93S 
        7.46        58.52        36.36        41.92         3.81 

$`12P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U TCGA-A8-A07E 
       23.80        11.28        11.97        11.05        29.03        19.99 
TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       15.06        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       50.24        17.79         5.65         2.56        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       98.33        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O 
       89.16         9.70        10.42        21.14        14.79        50.79 
TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       16.47        73.64        50.07        26.99        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SO TCGA-A1-A0SQ 
       47.24        31.79         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      143.15        18.02        78.41       121.94        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
      101.98        55.43       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        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       118.45        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-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-A0YG 
       18.90        20.75        32.55        25.28        18.21        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-A1G6 TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       19.20        16.47        18.15       105.34        10.59        36.23 
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        56.28        35.93 
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-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       35.31        34.29        35.47        37.45        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       20.19        25.15        29.56        23.74        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD 
       10.59        10.29        13.41        14.70        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VX 
       21.17        14.73        12.10        10.72         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02        13.02         1.02        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        17.03        53.98         9.01        43.00        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-A085 
        7.99        24.99         9.99        45.07        18.05        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-A08T TCGA-A8-A092 
       37.05         9.99        31.00        31.00       112.08        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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        19.23        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.26        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3BB 
       60.92        87.12        26.04        74.14        33.04        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       14.99        23.24        24.79        29.26        16.80        14.96 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       11.44        17.42        13.58        12.26         1.68         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-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-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF 
        7.36         7.46         0.33         0.33         0.33         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.17         6.90         7.04         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         5.36         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-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       66.77        95.70        68.75        58.95        44.42        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       21.53        50.86        76.77        65.10        26.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       115.27       113.62       108.72       106.78       102.31 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       97.08        61.87        82.62        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
      130.09        15.62        32.52       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 
      109.02        75.22        98.93        64.83        55.86       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL 
       83.87       134.14       107.21       125.16       103.86        97.68 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       96.00        86.07        93.90        99.32        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27       102.84       105.30        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       89.00        71.05       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      129.57        50.70        65.52       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM 
      129.07       140.88        68.45       212.25        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS 
      263.28       162.05       140.28       100.70        89.46        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.46        18.35        21.01       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
       73.51       170.17        37.87         7.07        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        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 
       25.55        63.09        81.44        39.16        70.22        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        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       74.89        61.68        72.23        74.14        76.60        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       77.75        49.94        74.14        89.06        81.73        77.98 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS 
       38.01        29.98        13.91        78.28        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30        44.81        81.83        24.49        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        63.39        53.26        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-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        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        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-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        91.99       113.82        82.85        42.28 
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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       25.08       120.62       114.15        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       33.99        63.35        55.00        45.63        53.98        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26        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-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A135 
       12.66        12.66        48.53        12.56        12.16        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.46        12.49        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.76        14.43        33.99        12.95        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        56.81        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-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        18.15        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-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        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-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.73        21.83        19.92        55.30        15.85        16.31 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        43.04        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-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48        17.06         1.61 
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        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        40.96        38.60        33.17        75.98 
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        69.34        69.96 
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-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        11.05        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE 
       76.57        53.62        87.22        33.01        28.50        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
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        75.81 
TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       28.90        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       38.76        34.29        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        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        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        41.72        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       38.99         1.94         7.13        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       26.70         0.79        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        28.77        25.94 
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-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
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-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        17.52        23.51        15.22 
TCGA-EW-A6SB TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       24.99         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        70.85        72.10        85.15       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX 
        2.10        36.30        31.99        58.62        34.92        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-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-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.26         9.93        18.81        18.48        21.07        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ 
       19.27        13.84        17.39        17.26        17.03        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            282.90             281.29 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             31.00              27.88 
[1] "0.2 - 282.9 (31.0)" "0.0 - 281.3 (27.9)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED        10        8        0        1        50        41
  12P LOSS WILD-TYPE      79       75        6        5       302       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         22          8          6        2
  12P LOSS WILD-TYPE         2        133         19         59       18
                    vv
clus                 STAGE X
  12P LOSS MUTATED         1
  12P LOSS WILD-TYPE      12
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                  8                 75
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                50                302
  STAGE IIB                41                212
  STAGE III                 0                  2
  STAGE IIIA               22                133
  STAGE IIIB                8                 19
  STAGE IIIC                6                 59
  STAGE IV                  2                 18
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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  90  16  13
  12P LOSS WILD-TYPE 242 535 121  27
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               32                242
  T2               90                535
  T3               16                121
  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  56  17   8
  12P LOSS WILD-TYPE 439 302 102  69
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               67                439
  N1               56                302
  N2               17                102
  N3                8                 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"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED   132   3
  12P LOSS WILD-TYPE 757  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    132    3
  12P LOSS WILD-TYPE  757   19
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0              132                757
  1                3                 19
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED   150   2
  12P LOSS WILD-TYPE 917  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    150    2
  12P LOSS WILD-TYPE  917   10
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE              150                917
  MALE                  2                 10
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    54  85
  12P LOSS WILD-TYPE 383 462
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     54   85
  12P LOSS WILD-TYPE  383  462
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                54                383
  YES               85                462
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P LOSS MUTATED                            0                           130
  12P LOSS WILD-TYPE                          1                           638
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P LOSS MUTATED                               11                   2
  12P LOSS WILD-TYPE                            190                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P LOSS MUTATED                       3                                3
  12P LOSS WILD-TYPE                     6                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  12P LOSS MUTATED                    1              2
  12P LOSS WILD-TYPE                 16             44
D64V9, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 130                638
  INFILTRATING LOBULAR CARCINOMA                 11                190
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  2                 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"
D64V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     7
  12P LOSS WILD-TYPE                                1    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          37    97
  12P LOSS WILD-TYPE                       144   647
D64V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      37                144
  WHITE                                          97                647
[1] 4 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     4 128
  12P LOSS WILD-TYPE  35 746
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4  128
  12P LOSS WILD-TYPE   35  746
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              128                746
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED   109  25
  12Q LOSS WILD-TYPE 808 123
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               134                931 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                123 
$`12Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A08F TCGA-AR-A1AR TCGA-AR-A2LL 
       19.20        21.73        22.32        33.01        17.23        66.15 
TCGA-BH-A18H TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A2-A04T 
       21.44        26.99        14.79        48.10        13.68        73.84 
TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 
       34.55        17.52        18.21        33.93        47.31        50.83 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       24.39        26.96        30.61        35.67        31.73        20.19 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.93        14.50        17.92        10.29         9.37        10.42 
TCGA-A8-A07G TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09Q TCGA-AC-A2QJ TCGA-AC-A3W7 
       18.97         0.99        43.00        25.02        14.66        15.48 
TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FL 
        8.22         1.12         1.78         0.16         7.00         7.59 
TCGA-AN-A0XO TCGA-AO-A0J4 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A124 
       12.33        52.18        50.70        72.00        55.33       115.27 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
      108.03        60.56        65.36       108.36       101.00        99.32 
TCGA-AR-A24K TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-B6-A0IG TCGA-B6-A0IH 
       50.89        99.62        93.30        93.83       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A1KF 
      233.62       255.68       234.28       102.77       282.90       101.52 
TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B7 TCGA-BH-A0BP 
      139.17        74.99        18.84        59.84        84.13        75.48 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E0 
       41.75        46.39        90.97        67.10         3.22         4.41 
TCGA-BH-A0EE TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1F6 TCGA-BH-A1FN 
       31.00        51.16        69.93        91.99        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 
       55.50        57.83        18.64        12.66        13.51        12.59 
TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JG TCGA-D8-A1XK 
       12.95        24.56        13.97        14.17        53.00        14.50 
TCGA-D8-A1XQ TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15E 
       16.41        16.04        40.41        63.62        25.05        20.71 
TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH 
       76.57        32.35        37.25        60.99        60.36       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1NH TCGA-E9-A1RG 
      102.61         8.75        34.92        17.69        18.94        21.27 
TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1OY TCGA-EW-A1P4 TCGA-EW-A1P8 
       40.73        30.44        26.40        29.85        29.82         7.86 
TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
        6.15        17.49        16.77        31.30        33.21         7.40 
TCGA-GM-A2DK TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
       86.96         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-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
      107.70        38.30        23.61        31.36        24.26        23.80 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E 
       11.28        11.97        11.05        53.06        29.03        19.99 
TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       15.06        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       45.07        29.98        16.57        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       13.71        50.24        17.79         5.65         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       19.20        98.33        57.27        73.35        81.63        54.05 
TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       32.58        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 
       50.79        16.47        73.64        50.07        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        31.79         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-A04W 
      143.15        18.02        78.41       121.94        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       56.28        35.93        50.37         7.30        21.30        23.21 
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-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       33.11        29.79        25.15        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB 
       11.34        10.59        10.29        13.41        14.70        13.74 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VY TCGA-A8-A06O 
       21.17        14.73        12.10        10.72         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I 
       17.03        53.98         9.01        43.00        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-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-A08I TCGA-A8-A08J 
        0.99        38.01        28.96        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00        31.00       112.08        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       19.33        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       24.13        25.05        14.99        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       16.80        14.96        11.44        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         7.46         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         6.90 
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 
        5.36         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        69.83        58.95        44.42 
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-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       53.03        21.53        50.86        76.77        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       62.04        71.80       113.62       108.72       106.78       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       97.08        61.87        82.62        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
      130.09        15.62        32.52       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        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       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      103.86        97.68        96.00        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       98.76        98.66        89.00        85.64        71.05       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25        81.17        78.02       263.28       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.28       100.70        89.46       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.46        18.35        21.01       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      245.10        28.27        68.94        58.55        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
      170.17        37.87         7.07        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        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.55        39.16        70.22        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       72.23        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       77.95        74.14        89.06        81.73        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       29.98        13.91        78.28        15.65         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        70.88        16.27        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        81.83        24.49        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        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-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-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB 
       49.58        17.69        25.81        31.53        25.08       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       122.83        33.99        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        45.63        53.98        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        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
      110.60        20.88        23.51         9.63         5.26        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-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.56        12.16        12.59        12.92        12.46        12.49 
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-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       15.45        16.87        16.70         0.03         9.76        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        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-A147 
       56.81        20.88        13.25        20.58        13.48        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        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF 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-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-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G 
       15.52         9.93        14.24        14.14        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        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        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        12.66        25.22        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        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        18.51        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       23.87        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        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       33.01        28.50        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL 
       54.18        19.66        24.59        75.81        28.90        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        38.76        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        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        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        24.82        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        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        46.65         6.58        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       41.72        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.18        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.95        40.41        41.13        39.78        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-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-GI-A2C9 
       34.03        17.52        23.51        15.22        24.99       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       85.15       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-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 
        2.60        62.47        11.84        11.57        21.24         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        10.62        32.75        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ 
       14.47        22.26         2.63        16.08        15.68        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        23.47        65.62        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-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
       18.48        21.07        20.68        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       17.26        17.03        66.84        29.03        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.16               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            282.90             281.29 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            31.515             27.250 
[1] "0.2 - 282.9 (31.5)" "0.0 - 281.3 (27.2)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         8        6        0        1        49        37
  12Q LOSS WILD-TYPE      81       77        6        5       303       216
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         16          7          7        2
  12Q LOSS WILD-TYPE         2        139         20         58       18
                    vv
clus                 STAGE X
  12Q LOSS MUTATED         1
  12Q LOSS WILD-TYPE      12
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   8                 81
  STAGE IA                  6                 77
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                49                303
  STAGE IIB                37                216
  STAGE III                 0                  2
  STAGE IIIA               16                139
  STAGE IIIB                7                 20
  STAGE IIIC                7                 58
  STAGE IV                  2                 18
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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  86  13  11
  12Q LOSS WILD-TYPE 249 539 124  29
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               25                249
  T2               86                539
  T3               13                124
  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    68  45  13   8
  12Q LOSS WILD-TYPE 438 313 106  69
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               68                438
  N1               45                313
  N2               13                106
  N3                8                 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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   116   2
  12Q LOSS WILD-TYPE 773  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    116    2
  12Q LOSS WILD-TYPE  773   20
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0              116                773
  1                2                 20
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   135   1
  12Q LOSS WILD-TYPE 932  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    135    1
  12Q LOSS WILD-TYPE  932   11
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE              135                932
  MALE                  1                 11
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    39  82
  12Q LOSS WILD-TYPE 398 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     39   82
  12Q LOSS WILD-TYPE  398  465
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                39                398
  YES               82                465
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q LOSS MUTATED                            0                           115
  12Q LOSS WILD-TYPE                          1                           653
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q LOSS MUTATED                               10                   3
  12Q LOSS WILD-TYPE                            191                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q LOSS MUTATED                       3                                2
  12Q LOSS WILD-TYPE                     6                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  12Q LOSS MUTATED                    0              3
  12Q LOSS WILD-TYPE                 17             43
D65V9, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 115                653
  INFILTRATING LOBULAR CARCINOMA                 10                191
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  3                 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"
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                          39    85
  12Q LOSS WILD-TYPE                       142   659
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                      39                142
  WHITE                                          85                659
[1] 4 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     5 115
  12Q LOSS WILD-TYPE  34 759
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5  115
  12Q LOSS WILD-TYPE   34  759
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              115                759
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   357  67
  13Q LOSS WILD-TYPE 560  81
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               424                641 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                67                 81 
$`13Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A0CD TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A06T 
       19.20        38.30        31.36        21.73        22.32        53.06 
TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 
       29.03        33.01        33.01        45.07        29.98        16.57 
TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O 
       19.79        13.71        50.24        17.79         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A18H 
       19.20        17.23        66.15        73.35        81.63        21.44 
TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 
        9.70        21.14        50.79        73.64        50.07        26.99 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LD-A74U TCGA-LL-A5YP TCGA-Z7-A8R5 TCGA-3C-AAAU 
       52.96        75.02        13.22        14.79       108.07       133.05 
TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN 
      131.67        14.37        43.43        20.88        13.68        39.32 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04X 
       28.01        18.21        18.02        78.41        87.25        55.43 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79       114.81        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO 
      107.93        56.81        67.33        34.55        25.22        80.28 
TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YE 
       74.40        34.29        31.82        27.12        44.88        18.21 
TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A3XT 
       49.48        48.46        31.73        23.77        23.47        91.07 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       56.28        47.31         7.30        24.39        26.96        21.14 
TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3IZ 
       30.61        29.79        31.73        25.15        23.74        10.59 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.93        14.50        17.92        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
        8.75        13.02        17.98        26.01         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
        9.01        43.00        18.97        32.05         9.99        10.98 
TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L 
        9.99        36.95        13.02        38.01        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B 
       31.00        31.00        43.00        30.97         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 
       33.07         1.02        25.02        14.01        19.04        13.02 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH 
       27.02        38.04        22.95        73.05        99.35        33.04 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AC-A6IW 
       14.66        32.45        29.26        16.80        17.42        13.58 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
        8.22         0.03        20.19         0.33         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FS 
        1.78         1.71         9.96         0.33         0.33         6.90 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33         0.33         5.36         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J3 
        5.59        80.28        66.77        81.63        68.75        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       52.18        37.48        76.77        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ 
      115.27       108.03        70.42        60.56        53.88        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TP 
       82.62        11.51        24.79       130.09        15.62       140.55 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 
        5.26        75.22        64.83       107.24        65.36        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AW 
      107.21       125.16       108.36       101.00       103.86        86.53 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24S 
       33.73        50.89        94.22        99.78       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      105.27       105.30        50.96        98.66        99.62        93.30 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB 
       71.05        93.83        54.21        10.59        77.62       129.57 
TCGA-B6-A0IE TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RQ 
       65.52       140.88        68.45        81.17       102.77       140.28 
TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X5 
      282.90        97.48        79.46        18.35        21.01        68.94 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       85.35        68.12        18.84        59.84        25.55        63.09 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BP 
       39.55        84.13        37.22        32.02        21.70        75.48 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       76.60        49.94        77.95        74.14        41.75        46.39 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       90.97        81.73        38.01        13.91        78.28        15.65 
TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 
        4.41        81.83        31.00        10.78        15.16        23.08 
TCGA-BH-A0HB TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA 
       26.50        12.89        27.25         5.59        23.93        23.05 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       90.84        26.66        55.63        66.05         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       69.93        42.28        12.00        17.69        25.81        97.48 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FU 
      114.15        33.17        74.73        33.99        63.35        55.50 
TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12M 
       26.14       130.16        36.79        23.51         9.63        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A135 TCGA-C8-A1HF 
       12.66        11.77        12.66        48.53        12.92        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        11.28        12.03        12.33        12.95        20.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-C8-A8HR 
       12.36        12.95        16.70         9.76        12.95        13.41 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        13.97        14.17        13.48 
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 
       53.00        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        17.06        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        63.62        69.96        21.04 
TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       25.05        18.21        11.05        19.56        56.94        14.07 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1LK TCGA-E2-A1LL 
       76.57        33.70        22.19        60.99         8.75        43.04 
TCGA-E2-A56Z TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
        8.28        34.29        22.29        36.20        36.56        35.77 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
       18.94         9.86        11.15        45.01        32.09         1.12 
TCGA-E9-A1RG TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 
       21.27        41.72        40.73        40.50        38.99         7.13 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        30.18        23.84        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 
       12.20        25.94        22.82        29.85        40.41        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FS 
        7.86        18.90         6.15        14.43        19.96        52.73 
TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       17.49        15.22        79.10        83.34        70.85        72.10 
TCGA-GM-A2DL TCGA-GM-A3NW TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U TCGA-LL-A5YM 
      115.69       110.50        69.30         2.60        21.24        15.32 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D7 
       14.47        22.26        16.08        19.53        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-A5DC TCGA-PE-A5DD TCGA-S3-A6ZH TCGA-S3-AA10 
       26.04        17.36        47.01        64.21        21.07        19.27 
TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-XX-A89A 
       17.39        17.03        66.84        16.04 

$`13Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A7-A426 
      107.70        23.61        24.26        23.80        11.28        11.97 
TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       11.05        19.99        15.06        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AQ-A0Y5 TCGA-AR-A1AM TCGA-AR-A2LR 
       49.05        14.53        19.33         5.65        98.33        57.27 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1BC 
       54.05        32.58        89.16        10.42        14.79        16.47 
TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 
       15.68        85.35        24.95        29.23        25.05        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AALJ 
       40.08        18.87        13.94        11.41        52.96        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG 
       47.61        11.44         9.96         8.52        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T 
       47.24        31.79         7.96       143.15       121.94        73.84 
TCGA-A2-A04W TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0D2 
      101.98       136.73        99.12        92.48       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       118.45        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-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A1FW 
       50.47        21.90        21.67        18.61        19.33        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.20        16.47        52.47 
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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XY TCGA-A2-A3XZ 
       39.65        33.93        29.98        32.75        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       50.83        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-A13H 
       35.47        37.45        35.67        33.11        20.19        29.56 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB 
       20.61        11.34        10.29        13.41        14.70        13.74 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A8-A06P TCGA-A8-A06Q 
       21.17        14.73        12.10        10.72        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07R 
       31.00        17.03        18.97        14.01        12.00         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A08A TCGA-A8-A08C 
        7.99        24.99        45.07        18.05         0.99        28.96 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       19.96        37.05         0.99       112.08        40.01        41.98 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00         9.99        50.04         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        19.23 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       73.91         5.72        22.26        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3EH 
       60.92        87.12        26.04        74.14        19.33         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV 
       15.48        23.24        24.79        14.96        11.44        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03Y 
       12.26         1.68         1.12         1.32         2.30         0.33 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        0.23         0.62         7.36         7.46         0.16         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-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XP 
        7.04         0.33         0.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T 
        0.33         0.33         0.33        61.35        95.70        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       58.95        44.42        32.78        26.04        20.32        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        65.10 
TCGA-AO-A0JG TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       26.24       113.62       108.72       106.78       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04J TCGA-AQ-A1H3 
       82.68        40.57        20.45        97.08        26.93        32.52 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U1 
       98.33        84.10       109.02        98.93        55.86       133.22 
TCGA-AR-A0U3 TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      134.14        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24M 
       37.81        94.29        61.28        86.43       160.90       120.33 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 
      118.59         2.76       112.77       102.84        98.76        89.00 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       85.64       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       39.39        40.54        33.30        38.96       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       11.90       275.87        50.70       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE 
       18.77       127.33        84.59       165.76       129.07       255.68 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RS 
      212.25       234.28        78.02       263.28       162.05       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       89.46       169.51       188.68       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A40B 
      245.10        28.27        58.55         7.07        74.99       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 
       71.15        62.93        20.45        81.44        39.16        70.22 
TCGA-BH-A0B9 TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM 
       51.68        18.21        43.53        61.51        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0C3 TCGA-BH-A0DE 
       72.23        74.14        85.87        77.75        89.06        77.98 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       67.10        29.98         3.22         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27        15.68        14.30         9.63        44.81 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        63.32        30.35        63.39        53.26        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 
       32.91         4.90        35.93        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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FG 
       55.69        49.58        31.53        25.08       120.62       122.83 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A203 
       55.00        45.63        72.07        53.98        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        57.83        36.82        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       20.88        18.64         5.26        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.93        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-A137 
       12.56        12.16        13.51        12.59        12.59        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26W TCGA-C8-A26Z 
       12.49        12.33         0.16        12.33        12.53        15.45 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP 
       16.87         0.03        24.56        14.43        33.99        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        55.50        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        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F 
       16.64        15.16        43.04        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        48.03        16.41        13.48         1.61 
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        12.66        25.22        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        75.98        43.33        34.26        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15A 
       69.34        18.51        23.24        19.43        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       53.92         9.04        20.58        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU 
       70.36        33.73        28.44        59.18         3.88        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      106.75       102.61        34.55        43.56        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       38.76        17.69        34.82        32.88        36.82        34.16 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        41.62        35.24        25.84        24.82        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        48.23        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A243 
       42.25        37.74        39.09        38.37        41.03        20.12 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69         1.94        24.56        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX 
       32.91        30.44        23.90        26.70         0.79        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 
        8.48        18.21        18.90        13.25        16.57        28.77 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV 
       19.99        13.94        10.52        34.55        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB 
       22.09        34.03        17.52        23.51        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG 
       85.15        86.96       106.06       101.62        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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       11.57         7.10        13.28        10.62        32.75        17.06 
TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-LL-A9Q3 
       14.70         2.63        15.68         7.46        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RV 
       27.91        22.39         2.10        36.30        31.99        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P 
       28.87        24.72        26.70        65.62        42.77        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX 
       28.21        19.73        40.11         8.91        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        18.81        18.48        20.68        13.84 
TCGA-S3-AA15 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       17.26         3.81        29.03        15.35       107.05 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            282.90             281.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            27.005             28.770 
[1] "0.0 - 282.9 (27.0)" "0.0 - 281.3 (28.8)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        33       29        1        1       153       102
  13Q LOSS WILD-TYPE      56       54        5        5       199       151
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1         63          9         22        8
  13Q LOSS WILD-TYPE         1         92         18         43       12
                    vv
clus                 STAGE X
  13Q LOSS MUTATED         4
  13Q LOSS WILD-TYPE       9
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  33                 56
  STAGE IA                 29                 54
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA               153                199
  STAGE IIB               102                151
  STAGE III                 1                  1
  STAGE IIIA               63                 92
  STAGE IIIB                9                 18
  STAGE IIIC               22                 43
  STAGE IV                  8                 12
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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    97 259  58  15
  13Q LOSS WILD-TYPE 177 366  79  25
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               97                177
  T2              259                366
  T3               58                 79
  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
  13Q LOSS MUTATED   207 137  51  27
  13Q LOSS WILD-TYPE 299 221  68  50
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              207                299
  N1              137                221
  N2               51                 68
  N3               27                 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"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   354   9
  13Q LOSS WILD-TYPE 535  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    354    9
  13Q LOSS WILD-TYPE  535   13
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              354                535
  1                9                 13
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   425   5
  13Q LOSS WILD-TYPE 642   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    425    5
  13Q LOSS WILD-TYPE  642    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              425                642
  MALE                  5                  7
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   164 224
  13Q LOSS WILD-TYPE 273 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    164  224
  13Q LOSS WILD-TYPE  273  323
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               164                273
  YES              224                323
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q LOSS MUTATED                            0                           337
  13Q LOSS WILD-TYPE                          1                           431
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q LOSS MUTATED                               59                   4
  13Q LOSS WILD-TYPE                            142                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q LOSS MUTATED                       5                               11
  13Q LOSS WILD-TYPE                     4                               19
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  13Q LOSS MUTATED                    2             11
  13Q LOSS WILD-TYPE                 15             35
D66V9, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 337                431
  INFILTRATING LOBULAR CARCINOMA                 59                142
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 19
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                 11                 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"
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0    23
  13Q LOSS WILD-TYPE                                1    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          83   277
  13Q LOSS WILD-TYPE                        98   467
D66V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                 37
  BLACK OR AFRICAN AMERICAN                      83                 98
  WHITE                                         277                467
[1] 4 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    11 337
  13Q LOSS WILD-TYPE  28 537
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  337
  13Q LOSS WILD-TYPE   28  537
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 28
  NOT HISPANIC OR LATINO              337                537
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   219  46
  14Q LOSS WILD-TYPE 698 102
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               265                800 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                46                102 
$`14Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A8-A08F 
       19.20        31.36        21.73        22.32        11.28        33.01 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       45.07        29.98        13.71         5.65         2.56        32.91 
TCGA-AR-A1AM TCGA-BH-A18H TCGA-LL-A5YP TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AAAU 
       98.33        21.44        14.79        13.94        52.96       133.05 
TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       48.46        31.79        18.02        73.84        87.25       101.98 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
        5.19       107.93        67.33        79.76        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YT 
       27.12        50.43        20.75        18.21        18.61        23.77 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 
       19.20        33.93        91.07        29.98        47.31        50.83 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       26.96        21.90        35.31        31.73        20.19        25.15 
TCGA-A7-A26G TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW 
       23.74        13.74        14.50        21.17        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Z 
       10.42         8.75        13.02         1.02        31.00         1.02 
TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08G 
       18.97        32.05         9.99         8.98         9.99        19.96 
TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09N TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A23C 
        9.99        12.00         1.02        21.04        17.03        19.23 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A6IW 
       73.05        99.35        33.04        14.66         6.48        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       115.27       108.03 
TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04L TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       60.56        82.62       130.09         5.26       109.02        75.22 
TCGA-AR-A0U0 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AP TCGA-AR-A1AQ 
       65.36       125.16       108.36       101.00        93.90        99.32 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A251 
       86.43        33.73       160.90       104.28       105.30        99.62 
TCGA-AR-A255 TCGA-AR-A256 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO 
       71.05        93.83        11.90       112.37       233.62       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WX 
      140.88       255.68        81.17        97.48        18.35        21.01 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A409 TCGA-BH-A0AU 
       43.59       101.52        73.51        37.87        18.84        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       59.84        20.45        39.55        70.22        84.13        51.68 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       43.53        61.51        21.70        77.95        74.14        46.39 
TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0H7 TCGA-BH-A0RX TCGA-BH-A0WA 
       90.97         4.41         9.63        23.08         5.59        23.05 
TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EY 
       32.91        55.63         7.36        51.39        55.69        17.69 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A202 TCGA-BH-A42T 
       97.48        25.08       114.15        74.73        26.14        10.52 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A1HF 
       18.64        11.93        11.77        12.66        12.59        10.92 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A27B TCGA-C8-A8HP 
       12.03        12.33        12.95        12.95        14.43        13.02 
TCGA-C8-A9FZ TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JL 
       19.46        13.97        15.78        53.00        20.09        20.09 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XG TCGA-D8-A1XK 
       19.40        21.01        27.58        18.15        14.73        14.50 
TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27I 
       55.30        16.64        12.99        16.54        14.14        14.43 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A108 TCGA-E2-A14R TCGA-E2-A14T 
       13.48        10.09        13.08        27.52        38.60        75.98 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F 
       18.51        63.62        21.04        25.05        23.34        21.63 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LE 
       11.05        19.56        76.57        33.73        33.70        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
      106.75       102.61         8.28        34.92        38.76        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       34.16        36.20        24.82         6.12         3.02        11.15 
TCGA-E9-A1RB TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A3HO 
       32.09        39.09        38.37        40.73        29.72        38.07 
TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 
       30.18        18.21        28.77        25.94        22.82        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3U0 
        7.86        14.43        19.96        55.00        25.91        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DH 
       17.52        23.51        24.99        33.21       109.87        72.10 
TCGA-GM-A2DK TCGA-GM-A3XL TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 
       86.96        69.30        18.12         2.60        11.57         7.10 
TCGA-LL-A441 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RZ TCGA-OL-A5S0 
       32.75        12.36        19.59        58.52        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-PE-A5DC TCGA-PL-A8LX 
       23.47        41.92        26.04        28.21        47.01         0.16 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-XX-A899 
       18.81        20.68        19.27        17.03         3.81        15.35 
TCGA-XX-A89A 
       16.04 

$`14Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A426 
      107.70        38.30        23.61        24.26        23.80        11.97 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S 
       11.05        53.06        29.03        19.99        15.06        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-AC-A3W5 TCGA-AC-A3W6 
       33.01        17.95         1.02        49.05        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A7U7 TCGA-AR-A1AR 
       14.53        19.33        50.24        17.79        19.20        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O 
       89.16         9.70        10.42        21.14        14.79        50.79 
TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       16.47        73.64        50.07        26.99        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALI 
       14.50        40.08        18.87        11.41       108.07       131.67 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
       39.32        28.01        18.21       143.15        78.41       121.94 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
      107.93        77.19        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 
      118.45        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-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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       22.45        20.25        16.47        52.47        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV 
       18.15       105.34        10.59        36.23        39.65        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        35.93        50.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       23.21        21.14        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY 
       35.67        33.11        29.79        29.56        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SF 
       10.59        10.29        13.41        14.70        14.93        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06Y 
       14.73        12.10        10.72        13.02        17.98        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98         9.01        43.00        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
       12.00        10.98         7.99        24.99        45.07        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I 
       36.95        13.02         0.99        38.01        28.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       37.05        31.00        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        30.97        41.98         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        33.07        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-A0A7 
        0.99        14.01        12.00        19.04        13.02         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       27.02        38.04        22.95        73.91         5.72        22.26 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        19.33        32.45        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       29.26        16.80        14.96        11.44        17.42        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-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.46         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-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.90         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 
        5.36        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        69.83        58.95        44.42 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        26.04        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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       26.24        62.04        71.80       113.62       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        82.68        70.42        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        61.87        11.51        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW 
       15.62        32.52       140.55        98.33        84.10        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       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AS 
      107.21       103.86        97.68        96.00        86.07        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       94.29        61.28        86.53        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
      102.84        50.96        98.76        98.66        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       65.52       146.50        18.77       127.33        84.59       129.07 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.28       100.70        89.46       282.90       169.51 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        79.46       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 
       28.27        68.94        58.55       139.17       170.17         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AY 
       85.35        74.99        68.12       103.63        71.15        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       63.09        81.44        39.16        37.22        32.02        18.21 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD 
       85.87        77.75        49.94        41.75        89.06        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
       16.27        15.68        14.30        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        63.32        30.35        10.78        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        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-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79        23.93        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN 
       37.74        30.28        37.55        66.05        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        12.00        49.58 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       25.81        31.53       120.62        33.17       122.83        33.99 
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        53.98        55.50 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        38.60        83.31        57.83       130.16        36.82 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       36.79        20.12       110.60        20.88        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O 
        5.26        18.87        21.76         9.44        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
       12.56        12.16        13.51        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HO 
       12.49        12.33        11.34        11.28         0.16        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.36        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        0.03         9.76        24.56        33.99        12.95        12.49 
TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       13.41        56.81        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        55.50 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK 
       18.15        18.90        12.03        14.01        18.97        20.12 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        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-A1XF 
       16.73        25.74        23.90        12.39        17.16        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        19.92        17.69        16.41        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        43.04        15.32        15.52         9.93        14.24 
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        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       17.06         1.61        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        12.66        25.22        43.00        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-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U 
       47.15        44.68        40.96        38.24        33.17        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        69.34        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       19.43        23.87        22.82        17.29        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R 
       12.92        55.63        53.92         9.04        20.58        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        37.25        77.65        37.41        70.36        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LK TCGA-E2-A1LL 
       60.36        19.66        24.59        75.81         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       34.55        43.56        30.61        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       32.88        36.82        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.24        25.84        18.94         9.86        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.56        48.23        45.01        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       42.25        37.74        41.03        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
        9.47        32.91        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OX TCGA-EW-A1OY 
        8.48        18.90        13.25        16.57        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG 
       18.90        19.99         6.15        13.94        10.52        34.55 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       52.73        22.09        34.03        15.22        16.77        31.30 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
        7.40        59.57       216.76        79.10        83.34        70.85 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       85.15       115.69       106.06       101.62       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW 
       43.73        66.38        72.03        13.55        62.47        11.84 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       21.24        13.28        10.62        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-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.53        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        34.92        36.36        28.87        24.72 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       26.70        65.62        42.77        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
       40.11         8.91        64.21        86.96         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ 
       18.48        21.07        13.84        17.39        17.26        66.84 
TCGA-WT-AB44 TCGA-Z7-A8R6 
       29.03       107.05 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.03               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            255.68             282.90 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            24.820             29.675 
[1] "0.0 - 255.7 (24.8)" "0.0 - 282.9 (29.7)"
[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        2        94        65
  14Q LOSS WILD-TYPE      70       63        6        4       258       188
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         36          5         16        7
  14Q LOSS WILD-TYPE         2        119         22         49       13
                    vv
clus                 STAGE X
  14Q LOSS MUTATED         4
  14Q LOSS WILD-TYPE       9
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 20                 63
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                94                258
  STAGE IIB                65                188
  STAGE III                 0                  2
  STAGE IIIA               36                119
  STAGE IIIB                5                 22
  STAGE IIIC               16                 49
  STAGE IV                  7                 13
  STAGE X                   4                  9
[1] 12  2
[1] TRUE
[1] "dimension of 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    52 176  31   8
  14Q LOSS WILD-TYPE 222 449 106  32
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               52                222
  T2              176                449
  T3               31                106
  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   141  77  30  17
  14Q LOSS WILD-TYPE 365 281  89  60
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              141                365
  N1               77                281
  N2               30                 89
  N3               17                 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"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   218   7
  14Q LOSS WILD-TYPE 671  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    218    7
  14Q LOSS WILD-TYPE  671   15
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              218                671
  1                7                 15
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   268   1
  14Q LOSS WILD-TYPE 799  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    268    1
  14Q LOSS WILD-TYPE  799   11
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE              268                799
  MALE                  1                 11
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   104 143
  14Q LOSS WILD-TYPE 333 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    104  143
  14Q LOSS WILD-TYPE  333  404
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               104                333
  YES              143                404
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q LOSS MUTATED                            0                           217
  14Q LOSS WILD-TYPE                          1                           551
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q LOSS MUTATED                               30                   5
  14Q LOSS WILD-TYPE                            171                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q LOSS MUTATED                       5                                4
  14Q LOSS WILD-TYPE                     4                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  14Q LOSS MUTATED                    1              6
  14Q LOSS WILD-TYPE                 16             40
D67V9, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 217                551
  INFILTRATING LOBULAR CARCINOMA                 30                171
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  6                 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"
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                          70   162
  14Q LOSS WILD-TYPE                       111   582
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                      70                111
  WHITE                                         162                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"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    12 215
  14Q LOSS WILD-TYPE  27 659
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12  215
  14Q LOSS WILD-TYPE   27  659
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              215                659
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   265  50
  15Q LOSS WILD-TYPE 652  98
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               315                750 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                 98 
$`15Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 
       19.20        31.36        24.26        21.73        22.32        11.28 
TCGA-A8-A06U TCGA-A8-A084 TCGA-A8-A093 TCGA-A8-A09C TCGA-AC-A62X TCGA-AO-A1KT 
       29.03        15.06        17.95         1.02        13.71        17.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AR TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-D8-A146 
        2.56        32.91        17.23        57.27        81.63        21.14 
TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-S3-AA17 TCGA-WT-AB41 TCGA-Z7-A8R5 
       73.64        26.99        14.79        13.94        52.96       108.07 
TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       48.46        20.88        28.01        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT 
       87.25       101.98        99.12        24.79        77.19        75.25 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET 
      107.93        56.81       134.40        80.28        79.76        35.05 
TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 
       63.29        54.64        27.12        44.88        50.43        17.52 
TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS 
       20.75        18.21        18.61        31.73        19.20        33.93 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S1 TCGA-A2-A4S3 
       29.98        47.31        50.83         7.30        26.96        21.90 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A4SD 
       30.61        35.67        29.79        31.73        20.19        14.50 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06Y 
       17.92        10.29         9.37        10.42        17.98        26.01 
TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A08I 
        1.02        53.98        43.00        18.97         8.98        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09N 
        9.99        31.00        43.00        30.97         9.99         1.02 
TCGA-A8-A09W TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A2QJ 
        0.99        17.03        22.95        73.05        26.04        14.66 
TCGA-AC-A3OD TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A0AJ TCGA-AN-A0AK 
       14.83        14.96        13.58        20.19         9.96         7.36 
TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        0.33         6.44         7.00         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS 
        0.33         0.33         0.33         0.33        12.33         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       80.28        61.35        37.48        20.32        53.03        72.00 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       55.33       108.03        60.56        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
       24.79         5.26       109.02        75.22        64.83        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       65.36       133.22       125.16       108.36       101.00        99.32 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V 
       86.53        33.73       104.28       112.77        97.84       105.30 
TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A2LK TCGA-B6-A0I1 
       50.96        98.66        89.00        93.83        54.21        77.62 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RG 
      129.57       112.37       233.62       165.76       255.68        68.45 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY 
      102.77       100.70       282.90        79.46        21.01       113.79 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A402 TCGA-B6-A408 
       43.59       101.52        73.51        37.87        74.99        68.12 
TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA 
       18.84        71.15        62.93        70.22        51.68        37.22 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       74.89        77.75        74.14        41.75        46.39        90.97 
TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0H7 
       15.65        70.88         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        32.91        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-A12Y TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK 
       12.66        48.53        12.92        12.49        10.92        12.03 
TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A8HP TCGA-D8-A13Z 
       12.95        12.95         9.76        24.56        13.02        20.88 
TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       13.97        14.17        17.49        18.90        12.03        53.00 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO 
       18.15        15.22        21.83        14.50        19.92        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       16.41        16.31        12.99        16.54        15.32         9.93 
TCGA-D8-A27M TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O 
       13.48        16.18        25.22        46.59        40.11        44.68 
TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G 
       34.26        63.62        69.96        19.43        25.05        18.21 
TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1L7 
       12.92        76.57        37.25        37.41        33.70        60.36 
TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N6 
       24.59         8.75        34.92        38.76        34.29        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1R4 TCGA-E9-A1RC TCGA-E9-A1RE 
       36.20        36.56        41.62         6.12        40.24        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22E 
        6.58        21.27        46.59        34.45        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 
       40.73         0.69        38.99         1.94         7.13        12.33 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       38.07        30.18        30.44         0.79        25.81        26.40 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PC 
       25.94        29.85        40.41        41.13         7.86         6.15 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A6SA 
       19.96        55.00        52.73        25.91        34.03        16.77 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL 
       24.99        33.21       109.87        72.10        69.30         2.60 
TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A8F5 
       11.57        32.75        14.70        22.26        16.08        19.59 
TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A66K TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZF 
       58.52        23.47        41.92        64.21        86.96        18.81 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-WT-AB44 
       18.48        19.27        29.03 

$`15Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A426 TCGA-A7-A5ZX 
      107.70        38.30        23.61        23.80        11.97        11.05 
TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09E 
       53.06        19.99        33.01        33.01        33.01        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       45.07        29.98        16.57        19.79        14.53        19.33 
TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A5QM 
       50.24         5.65        19.20        98.33        66.15        73.35 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 
       14.79        50.79        16.47        50.07        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G TCGA-3C-AAAU TCGA-3C-AALI 
       14.50        40.08        18.87        11.41       133.05       131.67 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       48.10        14.27        47.24        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CK 
       39.32        18.21       143.15       121.94        55.43       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D0 
      114.81        92.48       107.93         5.19        98.99        67.33 
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       118.45 
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-A1G6 TCGA-A2-A259 
       17.36        60.72        22.45        20.25        16.47        52.47 
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        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       39.65        91.07        32.75        56.28        35.93        50.37 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CG 
       24.39        21.30        23.21        21.14        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G 
       35.47        37.45        33.11        25.15        29.56        23.74 
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-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.93        13.74        21.17        14.73        12.10        10.72 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A075 
        8.75        13.02        13.02         1.02        31.00        17.03 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
        9.01        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-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-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       37.05        31.00         0.99       112.08        40.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q 
       12.00         9.99        12.00        50.04        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-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        27.02        38.04        19.23 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         5.72        22.26        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45         6.48        16.31        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       14.99        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       11.44        17.42        18.67        12.26         1.68         8.22 
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-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-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        7.46         0.16         0.33         0.33         5.65         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR 
        7.59         7.17         6.90         5.36         0.30         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        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        69.83        58.95        44.42        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       21.40        52.18        26.04        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JM 
       50.86        76.77        65.10        26.24        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
      115.27       113.62       108.72       106.78       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       82.68        70.42        53.88        40.57        20.45        97.08 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93       130.09        15.62        32.52       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       84.10        98.93       107.24        83.87       134.14       107.21 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      103.86        97.68        96.00        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       94.29        61.28        86.43       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U 
      120.33        99.78       118.59         2.76       105.27       102.84 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       98.76        99.62        93.30        85.64        71.05       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        86.53        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       33.30        38.96        10.59       143.38       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
      275.87        50.70        65.52       146.50        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
       84.59       129.07       140.88       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       140.28        89.46       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        18.35       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 
       28.27        68.94        58.55       139.17       170.17         7.07 
TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       85.35       103.63        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD 
       81.44        39.55        39.16        84.13        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 
       74.14        76.60        85.87        49.94        77.95        89.06 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       78.28         3.22         2.56        79.00        67.86        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68        14.30        44.81        81.83        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        24.56 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ 
       52.96        26.50        20.38         5.85         2.50        36.85 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G 
       51.32        23.93        24.95        42.35        23.05         4.90 
TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       35.93        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       66.05        51.16        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       17.69        25.81        31.53        25.08       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       74.73       122.83        33.99        63.35        55.00        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       55.50        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 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        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        12.56        12.16        13.51        12.59 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.59        12.46        12.33        11.34        11.28         0.16 
TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       12.33        12.33        20.25        12.53        12.36        15.45 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
       16.87        16.70         0.03        14.43        33.99        12.95 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        56.81        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        55.50        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-A1XM TCGA-D8-A1XR TCGA-D8-A1XT 
       12.39        17.16        14.73        17.69        15.85        16.64 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        43.04        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        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       17.06         1.61        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 
       33.37        18.51        21.67        12.66        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-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 
       32.02        31.96        69.34        18.51        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       23.87        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       32.35        28.50        77.65        70.36        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       19.66        75.81        28.90       106.75       102.61        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A9RU TCGA-E9-A1N3 
       34.55        43.56         8.28        30.61        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       32.88        36.82        34.16        39.55        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
        1.12        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
       38.37        40.50        20.12        24.56        29.72         9.47 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW 
       32.91        23.90        23.84        26.70        27.85        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-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       28.77        22.82        29.95        39.78        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       14.43        34.55        22.09        17.49        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       15.22        31.30         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62       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-A7W5 
       13.55        18.12        62.47        11.84        21.24         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ 
       13.28        10.62        17.06        15.32        14.47         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68         7.46        19.53        12.36        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
       22.39         2.10        36.30        31.99        58.62        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-AA14 TCGA-S3-AA15 
        9.93        21.07        20.68        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.03         3.81        66.84        15.35        16.04       107.05 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.33               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            282.90             281.29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             30.18              27.27 
[1] "0.3 - 282.9 (30.2)" "0.0 - 281.3 (27.3)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED        18       22        0        2       116        76
  15Q LOSS WILD-TYPE      71       61        6        4       236       177
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           1         49          4         16        7
  15Q LOSS WILD-TYPE         1        106         23         49       13
                    vv
clus                 STAGE X
  15Q LOSS MUTATED         3
  15Q LOSS WILD-TYPE      10
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 22                 61
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA               116                236
  STAGE IIB                76                177
  STAGE III                 1                  1
  STAGE IIIA               49                106
  STAGE IIIB                4                 23
  STAGE IIIC               16                 49
  STAGE IV                  7                 13
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    60 210  37   9
  15Q LOSS WILD-TYPE 214 415 100  31
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               60                214
  T2              210                415
  T3               37                100
  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   162  89  43  20
  15Q LOSS WILD-TYPE 344 269  76  57
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              162                344
  N1               89                269
  N2               43                 76
  N3               20                 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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   266   7
  15Q LOSS WILD-TYPE 623  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    266    7
  15Q LOSS WILD-TYPE  623   15
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              266                623
  1                7                 15
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   313   4
  15Q LOSS WILD-TYPE 754   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    313    4
  15Q LOSS WILD-TYPE  754    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              313                754
  MALE                  4                  8
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   122 169
  15Q LOSS WILD-TYPE 315 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    122  169
  15Q LOSS WILD-TYPE  315  378
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               122                315
  YES              169                378
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q LOSS MUTATED                            0                           252
  15Q LOSS WILD-TYPE                          1                           516
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q LOSS MUTATED                               34                   3
  15Q LOSS WILD-TYPE                            167                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q LOSS MUTATED                       5                               10
  15Q LOSS WILD-TYPE                     4                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  15Q LOSS MUTATED                    2             11
  15Q LOSS WILD-TYPE                 15             35
D68V9, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 252                516
  INFILTRATING LOBULAR CARCINOMA                 34                167
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 20
  MUCINOUS CARCINOMA                              2                 15
  OTHER, SPECIFY                                 11                 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"
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                          62   213
  15Q LOSS WILD-TYPE                       119   531
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                      62                119
  WHITE                                         213                531
[1] 4 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     9 258
  15Q LOSS WILD-TYPE  30 616
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9  258
  15Q LOSS WILD-TYPE   30  616
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              258                616
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   148  24
  16P LOSS WILD-TYPE 769 124
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               172                893 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                24                124 
$`16P LOSS MUTATED`
TCGA-A7-A0CD TCGA-A7-A13G TCGA-AC-A5EI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AR-A1AR 
       38.30        23.61        14.53        17.79         2.56        17.23 
TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LL-A50Y TCGA-S3-AA12 
       57.27        81.63        15.68        85.35        25.05        18.87 
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        91.07        21.30 
TCGA-A7-A0CG TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A4SD 
       34.29        30.61        35.67        31.73        25.15        14.50 
TCGA-A7-A56D TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07L 
       14.73         9.37        13.02        17.03        43.00        32.05 
TCGA-A8-A07S TCGA-A8-A08J TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        7.99        37.05        43.00        33.07         1.02        25.02 
TCGA-A8-A09W TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A3TM 
        0.99        73.05        99.35        40.57        90.71        25.05 
TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A046 TCGA-AN-A0AL 
       13.58         0.03        20.19         1.12         0.33         7.46 
TCGA-AN-A0AR TCGA-AN-A0FN TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AO-A0J8 TCGA-AO-A0JD 
        0.33         7.17         0.33         0.33        22.36        72.00 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12G TCGA-AQ-A1H3 TCGA-AR-A0U3 TCGA-AR-A1AH 
      108.03        98.27        53.88        32.52       134.14       125.16 
TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A24V 
       99.32       160.90        50.89       118.59       102.84       105.30 
TCGA-AR-A251 TCGA-B6-A0I5 TCGA-B6-A0IC TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RH 
       99.62       281.29        50.70       233.62       255.68       212.25 
TCGA-B6-A0RL TCGA-B6-A0X0 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-BH-A0BO 
       81.17       129.70        43.59       170.17        74.99        72.23 
TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0H5 
       41.75        77.98        38.01         4.41        14.30        53.26 
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        36.79        18.64        18.87        21.76 
TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
       12.16        12.46        12.36         9.76        14.43        33.99 
TCGA-D8-A1JC TCGA-D8-A1JN TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A27V TCGA-D8-A4Z1 
       15.78        20.38        13.32        14.70        12.53        21.67 
TCGA-D8-A73U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15R 
       16.18        32.02        69.34        63.62        25.05        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 
       14.07        51.39        76.57        33.70         3.88        60.36 
TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A22D 
        8.75        34.92        38.76        41.62        18.94        41.03 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A54Y TCGA-EW-A1J6 TCGA-EW-A1P8 
       40.73         0.69         1.94        23.84        28.77         7.86 
TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH 
        6.15        17.49        17.52        59.57        83.34        72.10 
TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-HN-A2OB TCGA-LL-A5YN 
       38.20        69.30        72.03         2.60        62.47        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66L TCGA-OL-A6VO 
       12.36        19.59        58.52        36.36        42.77        28.21 
TCGA-PE-A5DC TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-WT-AB44 
       47.01        20.68        19.27        29.03 

$`16P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
       19.56       107.70        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       19.99        15.06        33.01        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
        1.02        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 
       19.33        13.71        50.24         5.65        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       98.33        66.15        73.35        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O 
       89.16         9.70        10.42        21.14        14.79        50.79 
TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       16.47        73.64        50.07        26.99        52.96        75.02 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       13.22        24.95        29.23        14.79        14.50        40.08 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI 
       13.94        11.41        52.96       108.07       133.05       131.67 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
       48.46        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
      101.98        55.43       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 
       92.48        77.19         5.19       107.93        56.81        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       118.45 
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-A0SY 
       24.72        99.19        54.64        27.12        44.88        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-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       18.90        25.28        18.21        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-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 
       23.47        17.36        22.45        20.25        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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-A3XW 
       36.23        39.65        33.93        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CH 
       23.21        26.96        21.14        21.90        35.31        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G 
       37.45        33.11        29.79        20.19        29.56        23.74 
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-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.93        13.74        21.17        17.92        12.10        10.72 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.29        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F 
       31.00        26.01         1.02        53.98         9.01        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-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-A08I TCGA-A8-A08L 
        0.99        38.01        28.96        19.96        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
       31.00        31.00         0.99       112.08        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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-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-A2FE 
       19.23        22.95        73.91         5.72        22.26        86.66 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       24.13        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       16.80        14.96        11.44        17.42        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         8.22         1.32         2.30         0.33         0.33 
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-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.36         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.96         7.00         7.59         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         5.36        12.33 
TCGA-AN-A0XP TCGA-AN-A0XS 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-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 
       69.83        58.95        44.42        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        20.32        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        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       115.27       113.62       108.72       106.78       102.31 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       82.68        70.42        60.56        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       15.62       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        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 
      133.22        83.87       107.21       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.53        86.43        33.73        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       50.96        98.76        98.66        89.00        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       63.62        38.17        39.39        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38        11.90       275.87       129.57 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.52       146.50       112.37        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
      165.76       129.07       140.88        68.45       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       169.51        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       206.86       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 
       58.55       101.52        73.51       139.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        85.87        77.75        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.95        74.14        46.39        89.06        90.97        81.73 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       67.10        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        79.00        67.86        70.88        16.27        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        81.83        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 
       30.35        10.78        15.16        63.39        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-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       36.85        12.89        27.25         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        32.91         4.90        35.93 
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-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05         7.36        51.16        91.99       113.82 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       12.00        49.58        17.69        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       25.08       120.62        74.73       122.83        33.99        63.35 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07        53.98        55.50        28.14        26.14 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        57.83        36.82        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-AB28 TCGA-C8-A12L 
       20.88        23.51         9.63         5.26         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-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.59        12.92        12.49        12.33        10.92 
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        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.53        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       16.70         0.03        24.56        12.95        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        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        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        55.50        18.15        18.90        12.03        53.00 
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        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        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 
       48.03        16.41        13.48        17.06         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-D8-A73X 
       13.08        12.26        33.37        18.51        12.66        25.22 
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        75.98        43.33        34.26 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       31.96        18.51        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       23.87        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        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       11.05        19.56        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       43.04        34.55        43.56         8.28        30.61        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       17.69        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.20        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        24.82        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        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       41.72        40.50        20.12        38.99         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       34.03        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF 
       33.21         7.40       109.87       216.76        79.10        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       110.50 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       43.73        66.38        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       21.24         7.10        13.28        10.62        32.75        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-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        7.46        19.53        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        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-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-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        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       18.48        21.07        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        15.35        16.04       107.05 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            281.29             282.90 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            36.015             26.400 
[1] "0.0 - 281.3 (36.0)" "0.0 - 282.9 (26.4)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED        20       11        1        0        66        36
  16P LOSS WILD-TYPE      69       72        5        6       286       217
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         22          5         10        1
  16P LOSS WILD-TYPE         2        133         22         55       19
                    vv
clus                 STAGE X
  16P LOSS MUTATED         2
  16P LOSS WILD-TYPE      11
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 11                 72
  STAGE IB                  1                  5
  STAGE II                  0                  6
  STAGE IIA                66                286
  STAGE IIB                36                217
  STAGE III                 0                  2
  STAGE IIIA               22                133
  STAGE IIIB                5                 22
  STAGE IIIC               10                 55
  STAGE IV                  1                 19
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    43 103  20   7
  16P LOSS WILD-TYPE 231 522 117  33
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               43                231
  T2              103                522
  T3               20                117
  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  48  17  12
  16P LOSS WILD-TYPE 411 310 102  65
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               95                411
  N1               48                310
  N2               17                102
  N3               12                 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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   148   1
  16P LOSS WILD-TYPE 741  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    148    1
  16P LOSS WILD-TYPE  741   21
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              148                741
  1                1                 21
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   173   1
  16P LOSS WILD-TYPE 894  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    173    1
  16P LOSS WILD-TYPE  894   11
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE              173                894
  MALE                  1                 11
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    72  82
  16P LOSS WILD-TYPE 365 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     72   82
  16P LOSS WILD-TYPE  365  465
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                72                365
  YES               82                465
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P LOSS MUTATED                            0                           128
  16P LOSS WILD-TYPE                          1                           640
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P LOSS MUTATED                               31                   3
  16P LOSS WILD-TYPE                            170                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P LOSS MUTATED                       2                                4
  16P LOSS WILD-TYPE                     7                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  16P LOSS MUTATED                    0              6
  16P LOSS WILD-TYPE                 17             40
D69V9, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 128                640
  INFILTRATING LOBULAR CARCINOMA                 31                170
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  6                 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"
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                          41   108
  16P LOSS WILD-TYPE                       140   636
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                      41                140
  WHITE                                         108                636
[1] 4 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     7 142
  16P LOSS WILD-TYPE  32 732
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7  142
  16P LOSS WILD-TYPE   32  732
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              142                732
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   508  74
  16Q LOSS WILD-TYPE 409  74
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               582                483 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                74                 74 
$`16Q LOSS MUTATED`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A25A TCGA-A7-A0CD 
       48.56        48.36        63.12        88.60       107.70        38.30 
TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A5ZX 
       23.61        31.36        21.73        22.32        11.28        11.05 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       29.03        19.99        15.06        33.01        33.01        17.95 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
       50.24        17.79         2.56        98.33        17.23        66.15 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY 
       81.63        54.05        32.58        21.44        89.16         9.70 
TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 
       21.14        50.79        16.47        73.64        50.07        26.99 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A50Y TCGA-S3-AA12 
       15.68        52.96        85.35        13.22        25.05        18.87 
TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SD TCGA-A1-A0SE 
       11.41       108.07        47.61        11.44        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-A0CK TCGA-A2-A0CO 
      143.15       121.94        73.84        87.25       136.73       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 
       92.48       107.93        77.19        75.25        98.99        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-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SY 
       79.76        34.29        24.72        63.29        54.64        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       17.13        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       25.28        18.21        21.67        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3KC TCGA-A2-A3KD 
       23.47        60.72        20.25        52.47        36.23        39.65 
TCGA-A2-A3XT TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       91.07        21.30        21.90        34.29        35.47        30.61 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IZ 
       33.11        31.73        25.15        29.56        20.61        10.59 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZW 
       14.93        13.74        14.50        21.17        14.73        10.72 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X 
       10.29         9.37        13.02        13.02         1.02        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07L 
       17.03         9.01        43.00        18.97        12.00        32.05 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       10.98         8.98         7.99        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T 
       28.96        19.96        37.05        31.00        31.00       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B 
       43.00        40.01        30.97        41.98         9.99        12.00 
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        22.95        73.91        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        74.14        19.33         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A4ZE 
       22.19        24.13        25.05        14.99        15.48        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       16.80        14.96        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03        20.19         1.12         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         0.33         7.36         0.33         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        6.90         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         0.33        80.28        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       68.75        21.40        20.32        22.36        53.03        21.53 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       72.00        65.10        62.04       113.62       108.72       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KS 
      102.31        98.27        70.42        53.88        97.08        11.51 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
       15.62        32.52        75.22       107.24        83.87       134.14 
TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ 
      125.16       103.86        97.68        96.00        93.90        99.32 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S 
      160.90        50.89        99.78       118.59         2.76        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 
      105.27       102.84       105.30        98.76        99.62        85.64 
TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A5QN TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH 
       33.30       281.29       275.87       129.57        50.70       112.37 
TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      127.33       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WZ 
      234.28        81.17       169.51        97.48        18.35       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 
      129.70        58.55        43.59       170.17        74.99        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 
      103.63        71.15        62.93        59.84        25.55        81.44 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BO 
       70.22        84.13        37.22        43.53        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       75.48        74.14        85.87        41.75        46.39        89.06 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       77.98        38.01        13.91        15.65         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H0 
       44.81        81.83        24.49        31.00        30.35        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       63.39        53.26        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-A18F TCGA-BH-A18J TCGA-BH-A18K 
       24.95        42.35        44.81        32.91        20.12        90.84 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.74        30.28         7.36        51.39        69.93        91.99 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 
       82.85        42.28        12.00        55.69        17.69        31.53 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A202 
      114.15        33.17        74.73       122.83        55.00        26.14 
TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42V TCGA-BH-A5IZ 
      130.16        36.79        20.12        10.52        20.88        18.64 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12Y TCGA-C8-A12Z 
       18.87        21.76         9.44        11.77        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.16        12.46        12.49        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A278 
       11.28        12.95        12.53        12.36        16.70         9.76 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 
       14.43        33.99        12.49        56.81        20.88        20.58 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       13.48        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 
       53.00        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 
       55.30        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        48.03        16.41         1.61 
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-E2-A107 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O 
       12.66        34.42        40.41        40.11        28.44        44.68 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y 
       38.24        33.17        43.33        34.26        32.02        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       18.51        63.62        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       53.92         9.04        20.58        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IH 
       76.57        33.01        37.25        77.65        37.41        33.73 
TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA 
       33.70         3.88        11.08        54.18        60.36        24.59 
TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        8.75        34.55        43.56        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF 
       34.29        32.88        36.82        34.16        41.62        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 
       25.84        18.94        24.82        28.27         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        3.02        11.15        48.23        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22D 
       46.65        21.27        47.64        34.45        32.05        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       41.72        40.73        40.50         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y 
       24.56        12.33        29.72        38.07        30.44        23.84 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       26.40        27.85        12.20         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P6 TCGA-EW-A1P8 
       16.57        28.77        25.94        40.41        18.48         7.86 
TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 
        6.15        10.52        34.55        52.73        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD 
       17.52        23.51        15.22        16.77        31.30        33.21 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DN 
        7.40        59.57        83.34        72.10        85.15       101.62 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
      110.50        38.20        69.30        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A5YL 
        2.60        62.47        11.57        21.24        13.28        17.06 
TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        22.26        12.36        19.59        27.91        22.39 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
       36.30        58.52        31.99        58.62        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       28.87        20.38        65.62        41.92        42.77        26.04 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-S3-A6ZF TCGA-S3-A6ZG 
       28.21        19.73        47.01        64.21        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       20.68        19.27        29.03        15.35        16.04       107.05 

$`16Q LOSS WILD-TYPE`
TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A426 
       19.20        36.13        19.56        24.26        23.80        11.97 
TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-AQ-A0Y5 
       53.06        33.01         1.02        49.05        45.07         5.65 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-C8-A1HL TCGA-E2-A158 
       32.91        19.20        57.27        73.35        10.42        14.79 
TCGA-GM-A2DD TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       75.02        24.95        29.23        14.79        14.50        40.08 
TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA 
       13.94        52.96       133.05       131.67        48.46         9.96 
TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P 
        8.52        14.27        20.88        13.68        18.21        18.02 
TCGA-A2-A04Q TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CU 
       78.41       101.98        55.43        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       118.45        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-A0YF TCGA-A2-A0YG 
       50.43        17.52         8.38        49.84        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       49.48        18.61        23.77        17.36        22.45        19.20 
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        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         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-A26G TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SF 
       23.74        11.34        10.29        13.41        14.70        17.92 
TCGA-A7-A5ZV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z 
       12.10        10.42         8.75        17.98        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A07W 
       53.98        18.97        14.01         9.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R 
       45.07        18.05        36.95        12.00         9.99         0.99 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H 
       12.00         9.99        50.04         0.99        19.23         5.72 
TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3YI TCGA-AC-A3YJ 
       87.12        33.04        14.66        32.45        23.24        24.79 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       11.44        17.42         1.32         0.23         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        1.78         1.71         9.96         7.46         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT 
        0.33         6.44         5.65         7.96         7.59         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO 
        0.33         0.36         0.33         0.33         0.33        12.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
        5.33         5.59        61.35        69.83        58.95        44.42 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JC 
       32.78        52.18        26.04        37.48        50.70        50.86 
TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A128 
       76.77        26.24        55.33        71.80       115.27       106.78 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR 
       82.68        60.56        40.57        20.45        61.87        82.62 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       24.79        26.93       130.09       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       84.10       109.02        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 
      133.22       107.21       108.36       101.00        86.07        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       94.29        61.28        86.53        86.43        33.73        94.22 
TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
      120.33       104.28       112.77        50.96        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LQ TCGA-AR-A5QP 
       93.30        71.05        93.83        20.25        40.54        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG 
       10.59        77.62       143.38        11.90        65.52       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RN 
      233.62        18.77        84.59       165.76        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.28       100.70        89.46       282.90 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        79.46        21.01       113.79       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 
       68.94       101.52        73.51       139.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A409 TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 
       85.35        18.84        20.45        63.09        39.55        39.16 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       51.68        32.02        18.21        61.51        21.70        74.89 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C7 
       76.60        77.75        49.94        77.95        74.14        90.97 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DX 
       81.73        67.10        29.98        78.28         3.22        70.88 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       63.32        10.78        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18L 
       26.50         5.59        23.05         4.90        35.93        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        25.08       120.62        33.99 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        45.63        72.07        53.98        55.50        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A5J0 
       38.60        83.31        57.83        36.82       110.60        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
        9.63         5.26        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 
       12.66        12.66        12.66        12.66        12.66        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.59        12.59        12.92         0.16        12.03        12.33 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
       12.33        20.25        12.95        15.45        16.87         0.03 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 
       24.56        12.95        13.02        13.41        19.46        13.25 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF 
       13.97        14.17        19.20        16.50        55.50        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        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H 
       43.04        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-D8-A73X 
       14.43        13.48        17.06        10.09        12.26        25.22 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N 
       43.00        27.52        46.59        37.51        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 
       40.96        38.60        75.98        31.96        69.96        19.43 
TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 
       23.34        21.63        11.05        19.56        53.62        87.22 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN 
       32.35        28.50        70.36        28.44        59.18        22.19 
TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       60.99        19.66        75.81        28.90       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1N9 
       43.04         8.28        17.69        34.82        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1RC 
       36.56        39.55        35.77         9.86        34.95        40.24 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
        6.58        46.59        42.25        37.74        39.09        38.37 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       20.12        38.99         9.47        32.91        30.18        23.90 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OW 
       26.70         0.79        25.81        39.72        18.90        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.95        29.85        41.13        39.78        29.82        23.11 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PH 
       30.08        18.90        19.99        13.94        14.43        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DA 
       55.00        25.91        22.09        24.99       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A3XG 
       79.10        70.85        86.96       115.69       106.06        43.73 
TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM 
       66.38        11.84         7.10        10.62        32.75        15.32 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       14.47         2.63        16.08        15.68         7.46        19.53 
TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       17.49         2.10        24.72        22.32        26.70        23.47 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX 
       17.36        14.07        40.11         8.91        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26         9.93        21.07        13.84        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.03         3.81        66.84 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            281.29             282.90 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             29.03              26.70 
[1] "0.0 - 281.3 (29.0)" "0.0 - 282.9 (26.7)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        53       43        3        4       203       135
  16Q LOSS WILD-TYPE      36       40        3        2       149       118
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         81         11         37        7
  16Q LOSS WILD-TYPE         1         74         16         28       13
                    vv
clus                 STAGE X
  16Q LOSS MUTATED         8
  16Q LOSS WILD-TYPE       5
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  53                 36
  STAGE IA                 43                 40
  STAGE IB                  3                  3
  STAGE II                  4                  2
  STAGE IIA               203                149
  STAGE IIB               135                118
  STAGE III                 1                  1
  STAGE IIIA               81                 74
  STAGE IIIB               11                 16
  STAGE IIIC               37                 28
  STAGE IV                  7                 13
  STAGE X                   8                  5
[1] 12  2
[1] TRUE
[1] "dimension of 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   152 338  81  18
  16Q LOSS WILD-TYPE 122 287  56  22
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1              152                122
  T2              338                287
  T3               81                 56
  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   291 187  59  46
  16Q LOSS WILD-TYPE 215 171  60  31
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              291                215
  N1              187                171
  N2               59                 60
  N3               46                 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 409  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    480    8
  16Q LOSS WILD-TYPE  409   14
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              480                409
  1                8                 14
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   586   4
  16Q LOSS WILD-TYPE 481   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    586    4
  16Q LOSS WILD-TYPE  481    8
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE              586                481
  MALE                  4                  8
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   243 298
  16Q LOSS WILD-TYPE 194 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    243  298
  16Q LOSS WILD-TYPE  194  249
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               243                194
  YES              298                249
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q LOSS MUTATED                            0                           387
  16Q LOSS WILD-TYPE                          1                           381
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q LOSS MUTATED                              161                   3
  16Q LOSS WILD-TYPE                             40                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q LOSS MUTATED                       1                               18
  16Q LOSS WILD-TYPE                     8                               12
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  16Q LOSS MUTATED                    3             17
  16Q LOSS WILD-TYPE                 14             29
D70V9, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 387                381
  INFILTRATING LOBULAR CARCINOMA                161                 40
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 12
  MUCINOUS CARCINOMA                              3                 14
  OTHER, SPECIFY                                 17                 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"
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1    28
  16Q LOSS WILD-TYPE                                0    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          90   408
  16Q LOSS WILD-TYPE                        91   336
D70V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          28                 32
  BLACK OR AFRICAN AMERICAN                      90                 91
  WHITE                                         408                336
[1] 4 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    21 463
  16Q LOSS WILD-TYPE  18 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21  463
  16Q LOSS WILD-TYPE   18  411
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   21                 18
  NOT HISPANIC OR LATINO              463                411
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   483  89
  17P LOSS WILD-TYPE 434  59
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               572                493 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                89                 59 
$`17P LOSS MUTATED`
TCGA-5L-AAT0 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A2-A25A 
       48.56        19.20        63.12        36.13        19.56       107.70 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A5ZX 
       31.36        24.26        23.80        21.73        22.32        11.05 
TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A093 
       29.03        19.99        15.06        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62X 
        1.02        45.07        29.98        16.57        19.79        13.71 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A5QM 
        5.65         2.56        32.91        98.33        17.23        73.35 
TCGA-BH-A0B6 TCGA-BH-A18H TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A1L8 
       81.63        21.44        10.42        21.14        14.79        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LD-A74U 
       50.07        26.99        15.68        52.96        75.02        13.22 
TCGA-LL-A740 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AAAU TCGA-3C-AALI 
       14.50        13.94        11.41        52.96       133.05       131.67 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.46        47.61        11.44        14.37        43.43        48.10 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       47.24        20.88        31.79        39.32        28.01        18.21 
TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CK 
       18.02       121.94        73.84        87.25       101.98       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-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YE 
       44.28        49.84        20.52        20.75        32.55        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV TCGA-A2-A1FW 
       21.90        21.67        19.33        48.46        23.47        17.36 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A3XT 
       20.25        19.20        42.44        18.15        39.65        91.07 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        56.28        35.93        50.83         7.30        24.39 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       26.96        21.90        34.29        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       25.15        29.56        23.74        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       21.17        17.92        14.73         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 
       13.02         1.02        17.98        31.00         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L 
       53.98         9.01        43.00        18.97        14.01        32.05 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08L 
        8.98         9.99        36.95        13.02        38.01         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09M 
       31.00         0.99        43.00        30.97         9.99        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        19.23        22.95        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD 
       40.57        19.33        14.66        32.45         6.48        14.83 
TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62Y 
       24.13        14.99        15.48        29.26        16.80        17.42 
TCGA-AC-A7VB TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D 
        8.22         2.30         0.23         0.33         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.46         0.16         0.33         0.33         6.44 
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-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         0.33         5.59        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        95.70        68.75        69.83        44.42        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE 
       21.40        52.18        21.53        50.70        72.00        76.77 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G 
       62.04        71.80       108.72       108.03        82.68        53.88 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        82.62        11.51        24.79        26.93       130.09 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY 
       32.52       140.55         5.26       109.02        98.93        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
      108.36       101.00        96.00        99.32        37.81        94.29 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P 
       86.43        33.73       160.90        94.22       118.59         2.76 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 
       97.84       105.27       102.84       105.30        98.66        89.00 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM 
       85.64        71.05        93.83       166.42        86.53        63.62 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       11.90       129.57        65.52       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       127.33        84.59       165.76       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0RV 
       68.45       212.25       234.28       100.70       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X7 TCGA-B6-A1KN 
       97.48        79.46       113.79       206.86        58.55       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 
       74.99        68.12        18.84        59.84        25.55        81.44 
TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BM 
       70.22        51.68        37.22        32.02        43.53        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       75.48        74.14        76.60        77.95        74.14        46.39 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       81.73        77.98        29.98        13.91        78.28        15.65 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       70.88        16.27         4.41        14.30         9.63        81.83 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB 
       31.00        63.32        15.16        23.08        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F 
        5.85        13.61        12.89        24.95        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q 
        4.90        35.93        20.12        26.66        30.28        55.63 
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-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 
      113.82        42.28        12.00        17.69        97.48        25.08 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM 
       33.17        74.73       122.83        33.99        63.35        45.63 
TCGA-BH-A1FN TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        26.14        38.60        57.83       130.16 
TCGA-BH-A42T TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12M 
       10.52        18.64        23.51        18.87        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        11.77        12.66        12.66        48.53        12.56 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
       13.51        12.59        12.92        12.46        12.49        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       11.34         0.16        12.03        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       12.36        12.95        15.45         9.76        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       33.99        13.02        12.49        19.46        56.81        20.88 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.48        19.20        14.17        17.49        16.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       18.15        18.90        53.00        20.12        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA 
       21.01        13.32        18.58        16.73        23.90        27.58 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       15.22        21.83        14.50        19.92        17.69        16.41 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        12.99        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N 
       14.24        14.14        13.45        13.05        13.48        17.06 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 
       10.09        13.08        12.53        16.18        12.66        43.00 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
       40.11        28.87        38.24        33.17        75.98        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       21.04        25.05        23.34        20.71        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1IE 
       55.63        11.05        14.07        51.39        76.57        77.65 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L7 
       70.36        33.73        33.70        28.44        60.99        60.36 
TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A573 
       24.59        28.90        43.04        34.55         8.28        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.29        17.69        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1R4 
       36.56        39.55        41.62        35.24        18.94         6.12 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        45.01        32.09        46.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       47.64        34.45        42.25        39.09        38.37        41.03 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO 
       40.73         0.69        38.99        12.33        29.72        38.07 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        30.44        23.90         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 
       27.85        12.20        18.90        13.25        16.57        28.77 
TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
       25.94        40.41        29.82        23.11         7.86        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3E8 
       13.94        10.52        14.43        55.00        25.91        34.03 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        70.85        72.10        85.15 
TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YM 
      115.69        69.30        11.84         7.10        10.62        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       14.70        14.47         7.46        12.36        19.59        17.49 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RW 
       27.91        36.30        58.52        31.99        58.62        36.36 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       22.32        20.38        23.47        47.01        64.21        86.96 
TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 
       18.81        21.07        19.27        17.03         3.81        29.03 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

$`17P LOSS WILD-TYPE`
TCGA-5L-AAT1 TCGA-A2-A0CQ TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A3J1 TCGA-A7-A426 
       48.36        88.60        38.30        23.61        11.28        11.97 
TCGA-A8-A06T TCGA-A8-A091 TCGA-A8-A09E TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI 
       53.06        33.01        49.05        14.53        19.33        50.24 
TCGA-AO-A1KT TCGA-AQ-A7U7 TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0DO TCGA-BH-A0EA 
       17.79        19.20        66.15        57.27        54.05        32.58 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-E2-A15O TCGA-E2-A1BC TCGA-GM-A2DO TCGA-LL-A440 
       89.16         9.70        50.79        16.47        85.35        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-OL-A5RU TCGA-S3-AA12 TCGA-Z7-A8R5 
       29.23        25.05        14.79        40.08        18.87       108.07 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A2-A04N 
        9.96         8.52        14.27        13.68         7.96       143.15 
TCGA-A2-A04Q TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CS TCGA-A2-A0CX 
       78.41        55.43        99.12        92.48        77.19        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       33.76        61.58       101.72       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        31.82        61.94        99.19        54.64 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD 
       17.52        17.13         8.38        17.46        18.90        25.28 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX 
       50.47        49.48        18.61        31.73        23.77        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F 
       22.45        16.47        52.47        17.19       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RY 
       36.23        33.93        29.98        47.31        50.37        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       23.21        21.14        35.31        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       29.79        20.19        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A8-A06P 
       13.41        14.70        12.10        10.72        10.29        13.02 
TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       26.01        18.97        12.00         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       24.99        45.07        18.05         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       12.00        37.05        31.00       112.08        40.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09T 
       12.00         9.99        12.00        50.04        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23G 
       15.02         0.99        12.00        21.04        27.02        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        5.72        22.26        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TM 
       26.04        74.14        33.04        16.31        22.19        25.05 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79        14.96        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         6.90         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-A0JL TCGA-AO-A124 
       53.03        50.86        65.10        26.24        55.33       115.27 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
      113.62       106.78       102.31        98.27        70.42        60.56 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TS 
       40.57        20.45        97.08        15.62        98.33        84.10 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
       75.22        64.83        65.36       103.86        97.68        86.07 
TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N 
       93.90        61.28        86.53        50.89       120.33        99.78 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 
      104.28       112.77        50.96        98.76        99.62        93.30 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       20.25        54.21        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       38.96        10.59        77.62       143.38       281.29       275.87 
TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       50.70       129.07        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      102.77       140.28        89.46       188.68        18.35        21.01 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A40B 
       73.51       170.17        37.87         7.07        85.35       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 
       71.15        62.93        20.45        63.09        39.55        39.16 
TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BO 
       84.13        18.21        61.51        21.70        74.89        72.23 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       85.87        77.75        49.94        41.75        89.06        90.97 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       67.10        38.01         3.22         2.56        79.00        67.86 
TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       15.68        44.81        24.49        30.35        10.78        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HQ 
       53.26        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-A1FB TCGA-BH-A1FC 
       55.69        49.58        25.81        31.53       120.62       114.15 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       55.00        53.98        55.50        83.31        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8G0 
       20.12       110.60        20.88         9.63         5.26        21.76 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        9.44        11.77        12.66        12.66        12.66        12.16 
TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A273 
       12.59        12.33        11.28        12.33        12.95        16.87 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 
       16.70         0.03        12.95        13.41        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       13.97        14.17        55.50        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X8 
       20.09        20.09        12.20        14.70        17.79        25.74 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
       18.15        12.39        17.16        14.73        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27I 
       16.31        15.16        43.04        17.42        16.04        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       48.03        16.41         1.61        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       21.67        25.22        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R 
       37.51        28.44        47.15        44.68        40.96        38.60 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D 
       43.33        32.02        19.43        23.87        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R 
       21.63        53.92         9.04        20.58        19.56        56.94 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IF TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       37.41        59.18         3.88        22.19        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX 
       19.66        75.81       106.75       102.61         8.75        43.56 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1NG 
       30.61        38.76        34.82        32.88        35.77        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        24.82        28.27        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RH TCGA-E9-A227 TCGA-E9-A229 
       11.15        40.24         1.12        46.59        32.05        37.74 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       41.72        40.50        20.12         1.94         7.13        24.56 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY 
        9.47        32.91        23.84        26.70        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       18.21        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH 
       18.48        30.08        19.99         6.15        34.55        19.96 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA 
       52.73        22.09        17.49        17.52        23.51        16.77 
TCGA-GM-A2D9 TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       59.57        86.96       106.06       101.62       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-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A5YL 
       62.47        11.57        21.24        13.28        32.75        17.06 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-MS-A51U 
       22.26         2.63        16.08        15.68        19.53        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J 
        2.10        34.92        28.87        24.72        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-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       19.73        40.11         8.91         0.16         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ 
       18.48        20.68        13.84        17.39        17.26        66.84 
TCGA-XX-A899 
       15.35 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.16               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            282.90             281.29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             27.35              28.87 
[1] "0.2 - 282.9 (27.4)" "0.0 - 281.3 (28.9)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED        42       41        1        4       185       145
  17P LOSS WILD-TYPE      47       42        5        2       167       108
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         87         13         37       11
  17P LOSS WILD-TYPE         2         68         14         28        9
                    vv
clus                 STAGE X
  17P LOSS MUTATED         8
  17P LOSS WILD-TYPE       5
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  42                 47
  STAGE IA                 41                 42
  STAGE IB                  1                  5
  STAGE II                  4                  2
  STAGE IIA               185                167
  STAGE IIB               145                108
  STAGE III                 0                  2
  STAGE IIIA               87                 68
  STAGE IIIB               13                 14
  STAGE IIIC               37                 28
  STAGE IV                 11                  9
  STAGE X                   8                  5
[1] 12  2
[1] TRUE
[1] "dimension of 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   126 358  74  19
  17P LOSS WILD-TYPE 148 267  63  21
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1              126                148
  T2              358                267
  T3               74                 63
  T4               19                 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"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED   271 187  67  42
  17P LOSS WILD-TYPE 235 171  52  35
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              271                235
  N1              187                171
  N2               67                 52
  N3               42                 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"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   483  12
  17P LOSS WILD-TYPE 406  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    483   12
  17P LOSS WILD-TYPE  406   10
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              483                406
  1               12                 10
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   574   5
  17P LOSS WILD-TYPE 493   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    574    5
  17P LOSS WILD-TYPE  493    7
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              574                493
  MALE                  5                  7
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   243 279
  17P LOSS WILD-TYPE 194 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    243  279
  17P LOSS WILD-TYPE  194  268
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               243                194
  YES              279                268
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P LOSS MUTATED                            0                           432
  17P LOSS WILD-TYPE                          1                           336
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P LOSS MUTATED                               93                   5
  17P LOSS WILD-TYPE                            108                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P LOSS MUTATED                       5                               19
  17P LOSS WILD-TYPE                     4                               11
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  17P LOSS MUTATED                    6             18
  17P LOSS WILD-TYPE                 11             28
D71V9, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 432                336
  INFILTRATING LOBULAR CARCINOMA                 93                108
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               19                 11
  MUCINOUS CARCINOMA                              6                 11
  OTHER, SPECIFY                                 18                 28
[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"
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0    38
  17P LOSS WILD-TYPE                                1    22
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                         103   388
  17P LOSS WILD-TYPE                        78   356
D71V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          38                 22
  BLACK OR AFRICAN AMERICAN                     103                 78
  WHITE                                         388                356
[1] 4 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    21 474
  17P LOSS WILD-TYPE  18 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21  474
  17P LOSS WILD-TYPE   18  400
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   21                 18
  NOT HISPANIC OR LATINO              474                400
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   227  43
  17Q LOSS WILD-TYPE 690 105
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               270                795 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                43                105 
$`17Q LOSS MUTATED`
TCGA-A1-A0SP TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A8-A07E 
       19.20       107.70        31.36        24.26        21.73        19.99 
TCGA-A8-A084 TCGA-A8-A093 TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AQ-A0Y5 
       15.06        17.95        29.98        16.57        19.79         5.65 
TCGA-AQ-A54N TCGA-AR-A1AR TCGA-BH-A0B6 TCGA-BH-A18H TCGA-C8-A1HL TCGA-E2-A158 
        2.56        17.23        81.63        21.44        10.42        14.79 
TCGA-E2-A2P5 TCGA-GM-A2DD TCGA-LD-A74U TCGA-3C-AALJ TCGA-3C-AALK TCGA-A1-A0SK 
       26.99        75.02        13.22        48.46        47.61        31.79 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK 
       39.32        28.01        18.02        73.84        87.25       136.73 
TCGA-A2-A0CM TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 
       24.79       107.93        75.25        98.99        67.33        34.55 
TCGA-A2-A0EN TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YK 
      134.40        44.88        50.43        32.55        18.21        19.33 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       17.36        19.20        42.44        91.07        32.75        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ 
       50.83        24.39        26.96        21.90        34.29        30.61 
TCGA-A7-A13D TCGA-A7-A26G TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       31.73        23.74        13.74        14.50        21.17        14.73 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06R 
       10.29         9.37        10.42         8.75         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07L 
       31.00        53.98         9.01        43.00        14.01        32.05 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08X TCGA-A8-A09N TCGA-A8-A0A7 
        8.98        38.01        12.00        43.00         1.02         0.99 
TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W7 
       17.03        73.05        99.35        14.66        32.45        15.48 
TCGA-AC-A62Y TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A0AL TCGA-AN-A0AS 
       17.42         2.30         0.33         1.78         7.46         0.33 
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-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03V 
        0.33         0.33         0.33         0.33        66.77        44.42 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 
       32.78        21.40        52.18        72.00        55.33       108.03 
TCGA-AO-A12D TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AR-A0TP TCGA-AR-A0TY TCGA-AR-A0U1 
       82.68        82.62        11.51       140.55        55.86       133.22 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AQ 
      134.14       125.16       108.36       101.00        96.00        99.32 
TCGA-AR-A1AY TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A250 TCGA-B6-A0IB TCGA-B6-A0IH 
       33.73        97.84       102.84        89.00       129.57       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      233.62       165.76       140.88       255.68        68.45       212.25 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A408 
      100.70       282.90       113.79       101.52       139.17        68.12 
TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B9 
       18.84        59.84        25.55        81.44        70.22        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0C1 
       37.22        32.02        75.48        76.60        77.95        46.39 
TCGA-BH-A0DP TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE 
       15.65         4.41        14.30         9.63        81.83        31.00 
TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18G 
       23.08        26.50        13.61        12.89        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES 
       35.93        30.28        55.63        51.16        69.93       113.82 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FH 
       42.28        12.00        17.69        97.48        33.17        33.99 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5J0 TCGA-C8-A12L 
       45.63        72.07        57.83       130.16        23.51        11.93 
TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A131 
       11.77        11.77        12.66        12.66        12.56        13.51 
TCGA-C8-A137 TCGA-C8-A1HK TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27B 
       12.46        12.03        12.53        12.36         9.76        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A145 
       33.99        13.02        19.46        56.81        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        16.64 
TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27V TCGA-D8-A73U TCGA-E2-A14V 
       12.99        15.32        13.48        12.53        16.18        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1LL 
       25.05        18.21        11.05        76.57        33.70        43.04 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1NH TCGA-E9-A1RA TCGA-E9-A1RF 
       34.92        34.29        22.29        18.94        45.01         6.58 
TCGA-E9-A1RG TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 
       21.27        41.03         0.69        12.33        30.18        30.44 
TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 
        0.79        28.77        25.94        40.41        29.82         7.86 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       15.22        24.99        33.21         7.40       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DI TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YN 
       79.10        85.15        11.84         7.10        10.62        14.70 
TCGA-LL-A5YO TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
       14.47         7.46        58.52        36.36        20.38        23.47 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A89A 
       64.21        86.96        17.03         3.81        29.03        16.04 

$`17Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        48.36        63.12        36.13        88.60        19.56 
TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 
       38.30        23.61        23.80        22.32        11.28        11.97 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       11.05        53.06        29.03        33.01        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
        1.02        49.05        45.07        14.53        19.33        13.71 
TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL 
       50.24        17.79        32.91        19.20        98.33        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY 
       57.27        73.35        54.05        32.58        89.16         9.70 
TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 
       21.14        50.79        16.47        73.64        50.07        15.68 
TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       52.96        85.35        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      108.07       133.05       131.67        11.44         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-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
       13.68         7.96        18.21       143.15        78.41       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CS 
      101.98        55.43        99.12       114.81        92.48        77.19 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19       107.93        56.81        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        80.28       118.45        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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        27.12        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-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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       20.25        16.47        52.47        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XW 
       10.59        36.23        39.65        33.93        29.98        56.28 
TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       47.31        50.37         7.30        21.30        23.21        21.14 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       35.31        35.47        37.45        35.67        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        25.15        29.56        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV 
       10.29        13.41        14.70        14.93        17.92        12.10 
TCGA-A7-A5ZW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       10.72        13.02        13.02        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-A086 
       24.99         9.99        45.07        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
        0.99        28.96        19.96        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 
       31.00         0.99       112.08        40.01        30.97        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       12.00         9.99         9.99        12.00        50.04        33.07 
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-A0A9 TCGA-A8-A0AD 
       12.00        19.04        13.02        21.04        27.02        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB 
       19.23        22.95        73.91         5.72        22.26        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       33.04        19.33         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       24.13        25.05        14.99        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       16.80        14.96        11.44        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         6.90         0.33         5.36 
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        69.83 
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        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        71.80       115.27       113.62       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       20.45        97.08        61.87        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       15.62        32.52        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 
       75.22        98.93        64.83       107.24        65.36        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      107.21       103.86        97.68        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       94.29        61.28        86.53        86.43       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      112.77       105.27       105.30        50.96        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      281.29        11.90       275.87        50.70        65.52       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RL 
       18.77       127.33        84.59       129.07       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.28        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      169.51        97.48       188.68        79.46        18.35        21.01 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       43.59        73.51       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ 
       74.99       103.63        71.15        62.93        20.45        63.09 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       39.55        39.16        84.13        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       21.70        74.89        61.68        72.23        74.14        85.87 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.75        49.94        74.14        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       81.73        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       78.28         3.22         2.56        79.00        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       16.27        15.68        44.81        24.49        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        63.39        53.26        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW 
       52.96        20.38         5.85         2.50        36.85        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-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
       44.81        23.05        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EO 
       37.74        37.55        66.05         7.36        51.39        91.99 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 
       82.85        55.69        49.58        25.81        31.53        25.08 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62       114.15        74.73       122.83        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        28.14        26.14        38.60        83.31 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       18.64         9.63         5.26        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
       12.16        12.59        12.59        12.92        12.49        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34        11.28         0.16        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.33        20.25        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A140 
        0.03        24.56        12.95        12.49        13.41        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        13.97        14.17        55.50        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL 
       12.03        53.00        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        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.85        16.31        15.16        43.04        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        48.03        16.41        17.06         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.26        33.37        18.51        21.67 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        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        75.98 
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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       53.92         9.04        20.58        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       37.25        77.65        37.41        70.36        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       60.36        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      102.61         8.75        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       38.76        17.69        34.82        32.88        36.82        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        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        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC 
        6.12         3.02        11.15        48.23        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        1.12        46.65        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y 
       29.72         9.47        38.07        32.91        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OW 
        8.48        18.21        18.90        13.25        16.57        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.95        29.85        41.13        39.78        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08        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-EW-A6SA 
       22.09        34.03        17.49        17.52        23.51        16.77 
TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       31.30        59.57        83.34        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A5YL 
       62.47        11.57        21.24        13.28        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ 
       15.32        22.26         2.63        16.08        15.68        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       22.32        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-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       47.01         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       21.07        20.68        19.27        13.84        17.39        17.26 
TCGA-V7-A7HQ TCGA-XX-A899 TCGA-Z7-A8R6 
       66.84        15.35       107.05 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.33               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            282.90             281.29 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            25.745             28.500 
[1] "0.3 - 282.9 (25.7)" "0.0 - 281.3 (28.5)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED        20       24        0        1        91        63
  17Q LOSS WILD-TYPE      69       59        6        5       261       190
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         41          6         14        6
  17Q LOSS WILD-TYPE         2        114         21         51       14
                    vv
clus                 STAGE X
  17Q LOSS MUTATED         2
  17Q LOSS WILD-TYPE      11
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 24                 59
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                91                261
  STAGE IIB                63                190
  STAGE III                 0                  2
  STAGE IIIA               41                114
  STAGE IIIB                6                 21
  STAGE IIIC               14                 51
  STAGE IV                  6                 14
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    63 163  34  11
  17Q LOSS WILD-TYPE 211 462 103  29
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               63                211
  T2              163                462
  T3               34                103
  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  78  34  18
  17Q LOSS WILD-TYPE 367 280  85  59
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0              139                367
  N1               78                280
  N2               34                 85
  N3               18                 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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   235   6
  17Q LOSS WILD-TYPE 654  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    235    6
  17Q LOSS WILD-TYPE  654   16
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0              235                654
  1                6                 16
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   272   0
  17Q LOSS WILD-TYPE 795  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    272    0
  17Q LOSS WILD-TYPE  795   12
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE              272                795
  MALE                  0                 12
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   107 138
  17Q LOSS WILD-TYPE 330 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    107  138
  17Q LOSS WILD-TYPE  330  409
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO               107                330
  YES              138                409
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q LOSS MUTATED                            0                           214
  17Q LOSS WILD-TYPE                          1                           554
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q LOSS MUTATED                               36                   4
  17Q LOSS WILD-TYPE                            165                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q LOSS MUTATED                       5                                5
  17Q LOSS WILD-TYPE                     4                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  17Q LOSS MUTATED                    0              8
  17Q LOSS WILD-TYPE                 17             38
D72V9, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 214                554
  INFILTRATING LOBULAR CARCINOMA                 36                165
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  8                 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"
D72V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0    21
  17Q LOSS WILD-TYPE                                1    39
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          59   170
  17Q LOSS WILD-TYPE                       122   574
D72V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                 39
  BLACK OR AFRICAN AMERICAN                      59                122
  WHITE                                         170                574
[1] 4 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     9 218
  17Q LOSS WILD-TYPE  30 656
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9  218
  17Q LOSS WILD-TYPE   30  656
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              218                656
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   255  59
  18P LOSS WILD-TYPE 662  89
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               314                751 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                 89 
$`18P LOSS MUTATED`
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A3J1 TCGA-A8-A06U TCGA-A8-A084 TCGA-A8-A09E 
       31.36        24.26        11.28        29.03        15.06        49.05 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A5QM TCGA-BH-A0B6 
       16.57        19.79         5.65        32.91        73.35        81.63 
TCGA-BH-A18H TCGA-D8-A146 TCGA-E2-A158 TCGA-EW-A1P3 TCGA-LD-A74U TCGA-3C-AALI 
       21.44        21.14        14.79        52.96        13.22       131.67 
TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
       14.37        20.88        13.68        28.01        18.02       101.98 
TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
       55.43         5.19       107.93        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-A0YE TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT 
       18.21        21.90        49.48        19.33        48.46        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XT 
       17.36        60.72        19.20        17.19        18.15        91.07 
TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A13F TCGA-A7-A4SA TCGA-A7-A4SB 
       29.98        26.96        34.29        25.15        14.93        13.74 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A076 
       17.92        14.73        10.42        17.98        26.01        53.98 
TCGA-A8-A07G TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L 
       18.97        10.98         9.99        38.01        37.05         9.99 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       30.97        12.00        50.04        33.07         1.02        25.02 
TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2FO 
       14.01        19.04         5.72        90.71        26.04        74.14 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A5XU 
       14.66        32.45         6.48        15.48        16.80        14.96 
TCGA-AC-A62V TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X 
       11.44         0.03        20.19         1.12         2.30         0.33 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         9.96         7.36         7.46         0.16         0.33 
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-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 
       61.35        66.77        81.63        52.18        26.04        20.32 
TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A129 TCGA-AO-A12E TCGA-AQ-A04H TCGA-AQ-A04J 
       21.53        26.24       108.03        70.42        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AI 
      130.09        15.62       109.02        64.83        83.87       108.36 
TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24V 
       93.90        61.28        86.53       160.90       112.77       105.30 
TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A5QN TCGA-AR-A5QQ 
       50.96        93.30        71.05        93.83        33.30        10.59 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RP 
      233.62        18.77       165.76       212.25        81.17       102.77 
TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A1KN 
      100.70        79.46        18.35       113.79        73.51       139.17 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0BA 
       74.99        18.84        59.84        25.55        39.55        37.22 
TCGA-BH-A0BD TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C7 
       18.21        75.48        77.75        74.14        41.75        90.97 
TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 
       38.01        70.88         9.63        30.35        24.56        23.08 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18F 
       52.96        20.38        27.25        50.79        23.93        32.91 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       90.84        26.66        51.39        51.16        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        12.00        55.69        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A203 
       97.48        25.08        33.17        45.63        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12O TCGA-C8-A12P 
       83.31       130.16        18.64        23.51        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66        12.56        12.59        12.59        12.92 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.49        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        12.95        12.36        12.95        15.45        16.87 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 
       16.70         9.76        33.99        56.81        13.97        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        16.50        18.15        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA 
       18.97        20.09        19.40        20.38        18.58        27.58 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 
       21.83        19.92        15.85        12.99        16.54        14.14 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A107 TCGA-E2-A109 
       13.48        10.09        18.51        16.18        34.42        46.59 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14V 
       40.11        28.44        44.68        38.24        38.60        34.26 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15M 
       18.51        69.96        19.43        25.05        20.71        11.05 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK 
       76.57        37.25        33.73        60.99        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 
       43.04        34.55        34.92        38.76        17.69        32.88 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R6 TCGA-E9-A1RF 
       36.56        41.62        25.84        18.94        11.15         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS 
       21.27        47.64        41.72         1.94        12.33        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-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 
        7.86         6.15        14.43        55.00        25.91        17.52 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2DH TCGA-GM-A2DL TCGA-JL-A3YW TCGA-LD-A7W5 
       33.21         7.40        72.10       115.69        11.84         7.10 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A9Q3 
       10.62        32.75        15.32        22.26        12.36        17.49 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DD 
       27.91        36.30        20.38        26.04        19.73        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UU-A93S 
       86.96         0.16        18.81        21.07        19.27         3.81 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`18P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A26I 
       19.56       107.70        38.30        23.61        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A08F 
       22.32        11.97        11.05        53.06        19.99        33.01 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       33.01        33.01        17.95         1.02        45.07        29.98 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54N 
       14.53        19.33        13.71        50.24        17.79         2.56 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR TCGA-BH-A0DO 
       19.20        98.33        17.23        66.15        57.27        54.05 
TCGA-BH-A0EA TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A15O TCGA-E2-A1BC 
       32.58        89.16         9.70        10.42        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO 
       73.64        50.07        26.99        15.68        75.02        85.35 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU 
       24.95        29.23        25.05        14.79        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU 
       18.87        13.94        11.41        52.96       108.07       133.05 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE 
       48.46        47.61        11.44         9.96         8.52        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       48.10        14.27        47.24        31.79         7.96        39.32 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      136.73        99.12        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 
       77.19        75.25        98.99        56.81        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       35.05        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-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-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       21.67        18.61        31.73        23.47        22.45        20.25 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.47        52.47        42.44       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        33.93        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.14        21.90        35.31        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H 
       35.67        33.11        29.79        31.73        20.19        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       14.70        14.50        21.17        12.10        10.72        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X 
        9.37         8.75        13.02        13.02         1.02        31.00 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I 
        1.02        17.03         9.01        43.00        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-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       19.96        12.00        31.00        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        41.98        12.00         9.99         9.99 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        19.04        15.02         0.99        12.00        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        19.23 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       22.95        73.91        22.26        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN 
       86.66        60.92        87.12        33.04        19.33        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI 
       14.83        22.19        24.13        25.05        14.99        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79        29.26        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.68         8.22         1.32         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        0.62         1.78         1.71         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         6.90 
TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        7.04         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P 
        0.33         0.33         0.33         5.33         5.59        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        69.83        58.95        44.42        32.78        21.40 
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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       76.77        65.10        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      113.62       108.72       106.78       102.31        98.27        82.68 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       60.56        53.88        40.57        20.45        97.08        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       82.62        11.51        32.52       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       84.10        75.22        98.93        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK 
      133.22       134.14       107.21       125.16       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        99.32        37.81        94.29 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       104.28        97.84       105.27       102.84 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE 
       98.76        98.66        89.00        99.62        85.64       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       40.54        38.96        77.62       143.38       281.29        11.90 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.52       146.50       112.37 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      127.33        84.59       129.07       140.88       255.68        68.45 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
      234.28        78.02       263.28       162.05       140.28        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ 
      282.90       169.51        97.48       188.68        21.01       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 
      101.52       170.17        37.87         7.07        85.35        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        62.93        20.45        63.09        81.44 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       39.16        70.22        84.13        51.68        32.02        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       61.51        21.70        74.89        61.68        72.23        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 
       76.60        85.87        49.94        77.95        46.39        89.06 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       81.73        77.98        67.10        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       15.65         3.22         2.56        79.00        67.86        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
        4.41        15.68        14.30        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        63.32        10.78        15.16        63.39        53.26 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       41.00        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       12.89        51.32         5.59        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
       23.05         4.90        35.93        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1ES 
       30.28        55.63        37.55        66.05         7.36       113.82 
TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       82.85        49.58       120.62       114.15        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       33.99        63.35        55.00        72.07        53.98        55.50 
TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       26.14        57.83        36.82        36.79        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
      110.60        20.88         9.63         5.26        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12U TCGA-C8-A12V 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG 
       12.66        48.53        12.16        13.51        12.46        11.34 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
       12.33        20.25        12.53         0.03        24.56        14.43 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Z 
       12.95        13.02        12.49        13.41        19.46        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB 
       13.25        20.58        14.17        13.48        19.20        55.50 
TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JS 
       15.78        12.03        20.12        20.09        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-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-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        55.30        16.41        16.31        16.64        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       43.04        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        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       17.06         1.61        13.08        12.53        12.26        33.37 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       21.67        12.66        25.22        43.00        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T 
       37.51        28.87        47.15        40.96        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 
       43.33        32.02        31.96        69.34        63.62        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       21.04        23.87        23.34        22.82        17.29        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       33.01        32.35        28.50        77.65        37.41        70.36 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       54.18        60.36        19.66        24.59        75.81       106.75 
TCGA-E2-A1LI TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 
      102.61        43.56         8.28        30.61        34.29        34.82 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE 
       36.82        22.29        34.16        36.20        39.55        35.77 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.24         9.86        24.82        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        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        1.12        46.65        46.59        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       37.74        39.09        38.37        41.03        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
       20.12         0.69        38.99         7.13        24.56         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       38.07        32.91        30.18        30.44        23.90        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        26.40        27.85        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        28.77        22.82        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 
       52.73        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        24.99        31.30       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM 
       79.10        83.34        70.85        85.15        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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        62.47        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ 
       21.24        13.28        17.06        14.70        14.47         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U 
       16.08        15.68         7.46        19.53        19.59        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
        2.10        58.52        31.99        58.62        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-A6VR 
       41.92        42.77        17.36        14.07        28.21        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z 
        8.91        47.01         0.26         9.93        18.48        20.68 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-XX-A899 
       13.84        17.39        17.26        17.03        66.84        15.35 
TCGA-Z7-A8R6 
      107.05 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            233.62             282.90 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             24.41              31.00 
[1] "0.0 - 233.6 (24.4)" "0.0 - 282.9 (31.0)"
[1] "hr=" "2"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        25       23        0        0        98        75
  18P LOSS WILD-TYPE      64       60        6        6       254       178
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         48         15         26        6
  18P LOSS WILD-TYPE         2        107         12         39       14
                    vv
clus                 STAGE X
  18P LOSS MUTATED         1
  18P LOSS WILD-TYPE      12
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  25                 64
  STAGE IA                 23                 60
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                98                254
  STAGE IIB                75                178
  STAGE III                 0                  2
  STAGE IIIA               48                107
  STAGE IIIB               15                 12
  STAGE IIIC               26                 39
  STAGE IV                  6                 14
  STAGE X                   1                 12
[1] 12  2
[1] TRUE
[1] "dimension of 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    69 188  41  22
  18P LOSS WILD-TYPE 205 437  96  18
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               69                205
  T2              188                437
  T3               41                 96
  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   141 105  39  28
  18P LOSS WILD-TYPE 365 253  80  49
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              141                365
  N1              105                253
  N2               39                 80
  N3               28                 49
[1] 4 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   263   6
  18P LOSS WILD-TYPE 626  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    263    6
  18P LOSS WILD-TYPE  626   16
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              263                626
  1                6                 16
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   317   3
  18P LOSS WILD-TYPE 750   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    317    3
  18P LOSS WILD-TYPE  750    9
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              317                750
  MALE                  3                  9
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   129 157
  18P LOSS WILD-TYPE 308 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    129  157
  18P LOSS WILD-TYPE  308  390
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               129                308
  YES              157                390
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P LOSS MUTATED                            0                           249
  18P LOSS WILD-TYPE                          1                           519
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P LOSS MUTATED                               48                   3
  18P LOSS WILD-TYPE                            153                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P LOSS MUTATED                       4                                7
  18P LOSS WILD-TYPE                     5                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  18P LOSS MUTATED                    0              9
  18P LOSS WILD-TYPE                 17             37
D73V9, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 249                519
  INFILTRATING LOBULAR CARCINOMA                 48                153
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           4                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 23
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  9                 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"
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                          53   213
  18P LOSS WILD-TYPE                       128   531
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                      53                128
  WHITE                                         213                531
[1] 4 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    12 262
  18P LOSS WILD-TYPE  27 612
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12  262
  18P LOSS WILD-TYPE   27  612
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              262                612
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   263  52
  18Q LOSS WILD-TYPE 654  96
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               315                750 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                52                 96 
$`18Q LOSS MUTATED`
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A3J1 TCGA-A8-A06U TCGA-A8-A084 TCGA-A8-A09E 
       31.36        24.26        11.28        29.03        15.06        49.05 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A2LR 
       16.57        19.79        17.79         5.65        32.91        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A18H TCGA-D8-A146 TCGA-EW-A1P3 TCGA-LD-A74U 
       73.35        81.63        21.44        21.14        52.96        13.22 
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        91.07 
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-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-A6VV TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       10.29        10.42        17.98        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P 
       53.98        18.97         9.99        38.01        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
        0.99        30.97         9.99        12.00        50.04        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-A3EH TCGA-AC-A3W7 
       90.71        26.04        14.66        32.45         6.48        15.48 
TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       16.80        11.44        12.26         0.03        20.19         1.12 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.30         0.33         2.96         7.36         7.46         0.16 
TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XU 
        7.59         0.33         0.36         0.33         0.30         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JA 
       80.28        66.77        32.78        52.18        20.32        21.53 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
      108.03        82.68        70.42        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U1 TCGA-AR-A0U2 
       15.62        84.10       109.02        98.93       133.22        83.87 
TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S 
       93.90        61.28        86.53       160.90       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.30        50.96        89.00        99.62        93.30        71.05 
TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL 
       10.59        18.77       165.76       255.68       212.25        81.17 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KF 
      102.77       100.70        79.46        18.35       113.79       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AZ TCGA-BH-A0BA 
       73.51       170.17        74.99        18.84        63.09        37.22 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       18.21        61.51        75.48        77.75        77.95        74.14 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 
       90.97        38.01         3.22        30.35        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18F 
       52.96        20.38        12.89        27.25        23.93        32.91 
TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       90.84        51.39        51.16        69.93        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       12.00        17.69        25.81        31.53        97.48        25.08 
TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5J0 TCGA-BH-A8FZ 
       45.63        28.14        83.31       130.16        23.51        18.87 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A135 
       11.77        12.66        12.66        12.56        12.59        12.92 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.49        12.33        11.28         0.16        12.03        12.33 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 
        9.76        33.99        20.88        13.97        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        15.78        18.90        53.00        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL 
       20.09        20.38        18.58        27.58        21.83        19.92 
TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R 
       15.85        12.99        16.54        14.14        13.48        10.09 
TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E 
       18.51        16.18        34.42        46.59        40.11        28.44 
TCGA-E2-A14O TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 
       44.68        18.51        63.62        69.96        19.43        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH 
       23.34        20.71        11.05        76.57        37.25        33.73 
TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 
       60.99        28.90         8.75        43.04        34.55        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NH 
       38.76        17.69        32.88        36.56        41.62        18.94 
TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 
       11.15         6.58        21.27        47.64        41.72         1.94 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J1 
       12.33        29.72        23.84         0.79        12.20        18.90 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF 
       25.94        29.85        40.41         7.86         6.15        14.43 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       55.00        25.91        17.52        33.21         7.40       109.87 
TCGA-GM-A2DH TCGA-GM-A2DL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A441 
       72.10       115.69         2.60        11.84        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A9Q3 
       17.06        15.32        14.47        22.26        16.08        17.49 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ 
       27.91        36.30        20.38        26.04        28.21        19.73 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH 
       47.01        64.21        86.96         0.16        18.81        21.07 
TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A89A 
        3.81        29.03        16.04 

$`18Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A26I 
       19.56       107.70        38.30        23.61        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E TCGA-A8-A08F 
       22.32        11.97        11.05        53.06        19.99        33.01 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       33.01        33.01        17.95         1.02        45.07        29.98 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI TCGA-AQ-A54N TCGA-AQ-A7U7 
       14.53        19.33        13.71        50.24         2.56        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       98.33        17.23        66.15        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
        9.70        10.42        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LL-A440 
       50.07        26.99        15.68        75.02        85.35        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       29.23        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALJ 
       13.94        11.41        52.96       108.07       133.05        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF 
       47.61        11.44         9.96         8.52        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-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      136.73        99.12        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       77.19        75.25        98.99        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58        25.22       101.72        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       74.40        72.00        35.05        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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       20.25        16.47        52.47       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        33.93        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.14        21.90        35.31        35.47        30.61        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       33.11        29.79        20.19        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SD 
       11.34        10.59        10.29        13.41        14.70        14.50 
TCGA-A7-A5ZW TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.72         9.37         8.75        13.02        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       31.00         9.01        43.00        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-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       45.07        18.05        36.95        13.02         0.99        28.96 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X 
       19.96        12.00         9.99        31.00       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09R TCGA-A8-A09T 
       40.01        41.98        12.00         9.99         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       15.02        12.00        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        19.23        22.95        73.91        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK 
       73.05        99.35        40.57        86.66        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        33.04        19.33        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       24.13        25.05        14.99        23.24        24.79        29.26 
TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VB 
       14.96        17.42        18.67        13.58         1.68         8.22 
TCGA-AC-A8OR TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        1.32         0.33         0.23         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         9.96         0.33         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         6.90         7.04 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         5.36         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        61.35        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       95.70        68.75        69.83        58.95        44.42        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       26.04        37.48        22.36        53.03        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        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       115.27       113.62       108.72       106.78       102.31 
TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
       61.87        82.62        11.51        32.52       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
        5.26        75.22        64.83        55.86       107.24        65.36 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        99.32        37.81        94.29 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
      118.59         2.76       104.28       105.27       102.84        98.76 
TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       98.66        85.64        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.52       146.50       112.37       233.62 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI 
      127.33        84.59       129.07       140.88        68.45       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       263.28       162.05       140.28        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      169.51        97.48       188.68        21.01       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN 
      245.10        28.27        68.94        58.55        43.59       139.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       37.87         7.07        85.35        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 
       62.93        59.84        20.45        25.55        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       39.16        70.22        84.13        51.68        32.02        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        74.89        61.68        72.23        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       85.87        49.94        41.75        46.39        89.06        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       77.98        67.10        29.98        13.91        78.28        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        79.00        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        63.32        10.78        15.16        63.39        53.26 
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         4.90        35.93        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-A1FB TCGA-BH-A1FC 
      113.82        82.85        55.69        49.58       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       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       72.07        53.98        55.50        26.14        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       36.82        36.79        20.12        10.52       110.60        20.88 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
       18.64         9.63         5.26        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HF 
       48.53        12.16        13.51        12.59        12.46        10.92 
TCGA-C8-A1HG TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A27A 
       11.34        12.95        12.33        20.25        12.53        24.56 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       56.81        13.25        20.58        14.17        13.48        19.20 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       55.50        18.15        12.03        20.12        20.09        19.40 
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-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS 
       14.73        14.50        17.69        55.30        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        15.16        43.04        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-A27T TCGA-D8-A27V 
       48.03        16.41        17.06         1.61        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       12.26        33.37        21.67        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       27.52        40.41        37.51        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        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       32.02        31.96        69.34        23.24        21.04        23.87 
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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       53.92         9.04        20.58        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       77.65        37.41        70.36        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
        3.88        22.19        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A3DX TCGA-E2-A56Z 
       24.59        75.81       106.75       102.61        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       30.61        34.29        34.82        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.20        39.55        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 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       38.99         7.13        24.56         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        30.44        23.90        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       28.77        22.82        29.95        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-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        23.51        15.22        16.77        24.99        31.30 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       216.76        79.10        83.34        70.85        85.15 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       86.96       106.06       101.62       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        62.47 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A6FQ 
       11.57        21.24         7.10        13.28        14.70         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-MS-A51U 
       15.68         7.46        19.53        12.36        19.59        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
        2.10        58.52        31.99        58.62        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        18.48        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-XX-A899 TCGA-Z7-A8R6 
       17.39        17.26        17.03        66.84        15.35       107.05 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            255.68             282.90 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             23.51              31.00 
[1] "0.0 - 255.7 (23.5)" "0.2 - 282.9 (31.0)"
[1] "hr=" "1.5"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        23       26        0        0        98        70
  18Q LOSS WILD-TYPE      66       57        6        6       254       183
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         50         15         26        6
  18Q LOSS WILD-TYPE         2        105         12         39       14
                    vv
clus                 STAGE X
  18Q LOSS MUTATED         3
  18Q LOSS WILD-TYPE      10
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  23                 66
  STAGE IA                 26                 57
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                98                254
  STAGE IIB                70                183
  STAGE III                 0                  2
  STAGE IIIA               50                105
  STAGE IIIB               15                 12
  STAGE IIIC               26                 39
  STAGE IV                  6                 14
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    70 191  39  20
  18Q LOSS WILD-TYPE 204 434  98  20
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               70                204
  T2              191                434
  T3               39                 98
  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  98  43  29
  18Q LOSS WILD-TYPE 362 260  76  48
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              144                362
  N1               98                260
  N2               43                 76
  N3               29                 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"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   260   6
  18Q LOSS WILD-TYPE 629  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    260    6
  18Q LOSS WILD-TYPE  629   16
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              260                629
  1                6                 16
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   318   3
  18Q LOSS WILD-TYPE 749   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    318    3
  18Q LOSS WILD-TYPE  749    9
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              318                749
  MALE                  3                  9
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   118 169
  18Q LOSS WILD-TYPE 319 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    118  169
  18Q LOSS WILD-TYPE  319  378
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               118                319
  YES              169                378
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q LOSS MUTATED                            1                           246
  18Q LOSS WILD-TYPE                          0                           522
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q LOSS MUTATED                               53                   2
  18Q LOSS WILD-TYPE                            148                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q LOSS MUTATED                       5                                7
  18Q LOSS WILD-TYPE                     4                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  18Q LOSS MUTATED                    0              7
  18Q LOSS WILD-TYPE                 17             39
D74V9, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 246                522
  INFILTRATING LOBULAR CARCINOMA                 53                148
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 23
  MUCINOUS CARCINOMA                              0                 17
  OTHER, SPECIFY                                  7                 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"
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                          55   211
  18Q LOSS WILD-TYPE                       126   533
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                      55                126
  WHITE                                         211                533
[1] 4 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    13 262
  18Q LOSS WILD-TYPE  26 612
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13  262
  18Q LOSS WILD-TYPE   26  612
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 26
  NOT HISPANIC OR LATINO              262                612
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   167  29
  19P LOSS WILD-TYPE 750 119
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               196                869 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                29                119 
$`19P LOSS MUTATED`
TCGA-A7-A26I TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09I 
       21.73        53.06        33.01        33.01         1.02        45.07 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-C8-A1HL TCGA-3C-AALJ TCGA-5T-A9QA 
       17.79         5.65         2.56        10.42        48.46         9.96 
TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X 
       13.68        18.21        18.02        73.84        87.25        55.43 
TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0T3 TCGA-A2-A0T7 
       24.79       107.93        25.22        80.28        49.84        20.75 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XT TCGA-A2-A3XX 
       21.90        21.67        23.77        17.36        91.07        47.31 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SF 
       50.37        26.96        31.73        20.19        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A076 
       14.73        10.42         1.02        17.98        17.03        53.98 
TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08I 
       18.97        32.05         9.99         9.99        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09N TCGA-AC-A2BM 
       37.05        31.00        12.00         9.99         1.02        99.35 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A8OQ 
       26.04        33.04        11.44        12.26         8.22         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-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0U2 
       71.80        61.87        98.33        84.10        98.93        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S 
      134.14       101.00        99.32       160.90       112.77        97.84 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB 
       89.00        93.30        54.21        10.59        77.62       129.57 
TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A400 TCGA-B6-A402 
      165.76       100.70       101.52       139.17         7.07        74.99 
TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BG TCGA-BH-A0BT 
       68.12        18.84        59.84        39.55        61.51        77.75 
TCGA-BH-A0BW TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EB TCGA-BH-A0H0 TCGA-BH-A0H7 
       77.95         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        32.91        35.93        26.66 
TCGA-BH-A18S TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A204 
       66.05        12.00        25.08        72.07        55.50        83.31 
TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A135 
       11.77        11.77        12.66        12.66        12.56        12.92 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A26Z 
       12.49        10.92        12.03        12.95        12.95        15.45 
TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A1JC 
       24.56        13.02        12.49        19.46        56.81        15.78 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT 
       18.97        20.09        19.40        27.58        16.41        16.64 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A152 
       16.54        14.14        13.48        46.59        44.68        69.96 
TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 
       25.05        12.92        14.07        76.57        34.92        38.76 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1RC 
       22.29        35.24         9.86        24.82         2.56        40.24 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A3QA 
       46.59        34.45        41.03        40.73        29.72        30.18 
TCGA-E9-A5UO TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA 
       25.81        25.94        22.82        29.95        40.41        18.90 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-EW-A6S9 
        6.15        19.96        55.00        52.73        17.49        15.22 
TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GM-A2DC TCGA-GM-A2DH TCGA-LL-A6FP TCGA-LL-A7T0 
       16.77        33.21        83.34        72.10        22.26        12.36 
TCGA-MS-A51U TCGA-OL-A5D7 TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF 
       22.39        58.52        20.38        28.21         0.16        18.81 
TCGA-S3-AA14 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       17.39         3.81        66.84        29.03 

$`19P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        22.32        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09K 
       19.99        15.06        33.01        17.95        49.05        29.98 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
       16.57        19.79        14.53        19.33        13.71        50.24 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A2LR 
       32.91        19.20        98.33        17.23        66.15        57.27 
TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 
       73.35        81.63        54.05        32.58        21.44        89.16 
TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 
        9.70        21.14        14.79        50.79        16.47        73.64 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD 
      133.05       131.67        47.61        11.44         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
       43.43        48.10        14.27        47.24        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
        7.96        39.32        28.01       143.15        78.41       121.94 
TCGA-A2-A04W TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      101.98       136.73        99.12       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       77.19        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       118.45 
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-A1G6 
       23.47        60.72        22.45        20.25        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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-A3XW 
       36.23        39.65        33.93        29.98        32.75        56.28 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13H 
       37.45        35.67        33.11        29.79        25.15        29.56 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.74        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        14.93        13.74        21.17        12.10        10.72 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06X 
       10.29         9.37         8.75        13.02        13.02        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I 
       26.01         1.02         9.01        43.00        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       12.00        10.98         8.98         7.99        24.99        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-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-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       30.97        41.98         9.99        12.00        50.04        33.07 
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        19.23        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       22.26        73.05        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       87.12        74.14        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        16.80        14.96 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP 
       17.42        18.67        13.58         1.68         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-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR 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-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.90         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         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-A03O 
        0.33         0.33         5.33         5.59        80.28        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 
       68.75        69.83        58.95        44.42        32.78        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        65.10        26.24        62.04        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        82.68        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       20.45        97.08        82.62        11.51        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT 
      130.09        15.62        32.52       140.55         5.26       109.02 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       75.22        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       125.16       108.36       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        93.90        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      118.59         2.76       104.28       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 
       50.96        98.76        98.66        99.62        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       39.39        40.54        33.30        38.96       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       11.90       275.87        50.70        65.52       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      233.62        18.77       127.33        84.59       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       162.05       102.77       140.28        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      169.51        97.48       188.68        79.46        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 
       58.55        43.59        73.51       170.17        37.87        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      103.63        71.15        62.93        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       81.44        39.16        70.22        84.13        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        43.53        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       72.23        75.48        74.14        76.60        85.87        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         2.56        79.00        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EE 
       15.68        14.30         9.63        44.81        81.83        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       63.32        30.35        10.78        63.39        53.26        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-A0RX TCGA-BH-A0W3 
       13.61        36.85        12.89        51.32         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       24.95        42.35        44.81         4.90        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
       72.56        37.74        30.28        55.63        37.55         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-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-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       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       33.99        63.35        55.00        45.63        53.98        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        57.83       130.16        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       110.60        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26        18.87        21.76         9.44        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE 
       12.16        13.51        12.59        12.59        12.46        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V 
       11.34        11.28         0.16        12.33        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.53        12.36        16.87        16.70         0.03         9.76 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 
       14.43        33.99        12.95        13.41        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        13.97        14.17        13.48        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        55.50        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       53.00        14.01        20.12        20.09        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-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-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       15.85        16.31        12.99        15.16        43.04        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-A27N TCGA-D8-A27P 
       13.05        14.43        48.03        16.41        17.06         1.61 
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        12.66        25.22        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-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        75.98 
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        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       63.62        23.24        19.43        21.04        23.87        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       35.77        25.84        18.94        28.27        34.95         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        3.02        11.15        48.23        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
       46.65         6.58        21.27        47.64        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        38.07        32.91        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 
        8.48        18.21        18.90        13.25        16.57        28.77 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        41.13        39.78        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        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        17.52        23.51 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       79.10        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.57        21.24         7.10        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        15.32        14.70        14.47         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68         7.46        19.53        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW 
        2.10        36.30        31.99        58.62        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-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-PE-A5DE TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.48        21.07        20.68        19.27        13.84 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       17.26        17.03        15.35        16.04       107.05 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            165.76             282.90 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            24.805             29.230 
[1] "0.2 - 165.8 (24.8)" "0.0 - 282.9 (29.2)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED        15       11        1        1        66        47
  19P LOSS WILD-TYPE      74       72        5        5       286       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         30          5         11        7
  19P LOSS WILD-TYPE         1        125         22         54       13
                    vv
clus                 STAGE X
  19P LOSS MUTATED         2
  19P LOSS WILD-TYPE      11
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  15                 74
  STAGE IA                 11                 72
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                66                286
  STAGE IIB                47                206
  STAGE III                 1                  1
  STAGE IIIA               30                125
  STAGE IIIB                5                 22
  STAGE IIIC               11                 54
  STAGE IV                  7                 13
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    44 124  20   9
  19P LOSS WILD-TYPE 230 501 117  31
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               44                230
  T2              124                501
  T3               20                117
  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
  19P LOSS MUTATED    82  75  21  15
  19P LOSS WILD-TYPE 424 283  98  62
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               82                424
  N1               75                283
  N2               21                 98
  N3               15                 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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   163   7
  19P LOSS WILD-TYPE 726  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    163    7
  19P LOSS WILD-TYPE  726   15
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              163                726
  1                7                 15
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   194   3
  19P LOSS WILD-TYPE 873   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    194    3
  19P LOSS WILD-TYPE  873    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              194                873
  MALE                  3                  9
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    83 100
  19P LOSS WILD-TYPE 354 447
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     83  100
  19P LOSS WILD-TYPE  354  447
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                83                354
  YES              100                447
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P LOSS MUTATED                            0                           171
  19P LOSS WILD-TYPE                          1                           597
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P LOSS MUTATED                                8                   1
  19P LOSS WILD-TYPE                            193                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P LOSS MUTATED                       3                                5
  19P LOSS WILD-TYPE                     6                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  19P LOSS MUTATED                    4              4
  19P LOSS WILD-TYPE                 13             42
D75V9, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 171                597
  INFILTRATING LOBULAR CARCINOMA                  8                193
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 25
  MUCINOUS CARCINOMA                              4                 13
  OTHER, SPECIFY                                  4                 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"
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                          48   111
  19P LOSS WILD-TYPE                       133   633
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                      48                133
  WHITE                                         111                633
[1] 4 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     9 154
  19P LOSS WILD-TYPE  30 720
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9  154
  19P LOSS WILD-TYPE   30  720
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              154                720
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   138  25
  19Q LOSS WILD-TYPE 779 123
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               163                902 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                25                123 
$`19Q LOSS MUTATED`
TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09C TCGA-A8-A09I 
       22.32        53.06        33.01        33.01         1.02        45.07 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-C8-A1HL TCGA-5T-A9QA TCGA-A1-A0SQ TCGA-A2-A04U 
       17.79         5.65        10.42         9.96        18.21        87.25 
TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D1 TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T7 
       55.43        24.79        34.55        80.28        27.12        20.75 
TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A13E 
       21.90        23.77        17.36        19.20        91.07        20.19 
TCGA-A7-A56D TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L 
       14.73         1.02        17.98        53.98        18.97        32.05 
TCGA-A8-A07O TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A09M 
        9.99        19.96        12.00        31.00         9.99        33.07 
TCGA-A8-A09N TCGA-AC-A23C TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A7VB 
        1.02        19.23        99.35        26.04        11.44         8.22 
TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV 
        1.12         0.23         2.96         0.33         7.04         0.33 
TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J4 
        0.33        80.28        66.77        95.70        21.40        52.18 
TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AR-A0U2 
       72.00        55.33        71.80        61.87        24.79        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S 
      134.14       101.00        99.32       160.90       112.77        97.84 
TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0WX 
       93.30        54.21        10.59        77.62       129.57        21.01 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
      101.52       139.17         7.07        74.99        68.12        18.84 
TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DQ TCGA-BH-A0EB TCGA-BH-A0EE 
       77.75        41.75        90.97         3.22        24.49        31.00 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I 
       15.16        23.08        50.79        23.05        32.91        35.93 
TCGA-BH-A18S TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12P 
       66.05        55.50        83.31        18.64        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A1HF TCGA-C8-A26X TCGA-C8-A26Y 
       12.66        12.66        12.56        10.92        12.36        12.95 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A1JC 
        9.76        24.56        12.49        19.46        56.81        15.78 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ 
       53.00        18.97        20.09        19.40        27.58        16.41 
TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O 
       16.64        16.54        14.14        13.48        46.59        44.68 
TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 
       25.05        12.92        14.07        76.57        34.92        38.76 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R7 
       22.29        35.24         9.86        24.82         2.56        48.23 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 
       32.09        46.59        34.45        41.03        40.73         0.69 
TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A5UO TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       29.72        30.18        25.81        22.82        29.95        40.41 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-EW-A6SA 
       18.90         6.15        55.00        52.73        17.49        16.77 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RY 
       83.34        70.85        72.10        12.36        58.52        24.72 
TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 TCGA-UU-A93S TCGA-V7-A7HQ 
       28.21         0.16        18.81        17.39         3.81        66.84 
TCGA-WT-AB44 
       29.03 

$`19Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06U 
       23.80        21.73        11.28        11.97        11.05        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09K 
       19.99        15.06        33.01        17.95        49.05        29.98 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
       16.57        19.79        14.53        19.33        13.71        50.24 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR TCGA-AR-A2LL 
        2.56        32.91        19.20        98.33        17.23        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H 
       57.27        73.35        81.63        54.05        32.58        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
       89.16         9.70        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD 
       73.64        50.07        26.99        15.68        52.96        75.02 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP 
       85.35        13.22        24.95        29.23        25.05        14.79 
TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 
       14.50        40.08        18.87        13.94        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK 
      108.07       133.05       131.67        48.46        47.61        11.44 
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-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04W 
      143.15        18.02        78.41       121.94        73.84       101.98 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS 
      136.73        99.12       114.81        92.48       107.93        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        98.99       107.93        56.81        67.33 
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       118.45 
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-A0SW 
       61.94        24.72        63.29        99.19        54.64        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-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       31.73        23.47        60.72        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47        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-A3XW 
       36.23        39.65        33.93        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        21.90        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-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J 
       29.79        31.73        25.15        29.56        23.74        20.61 
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-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        17.92        12.10        10.72 
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-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-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-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-A08J TCGA-A8-A08L TCGA-A8-A08P 
        0.99        38.01        28.96        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 
        0.99       112.08        43.00        40.01        30.97        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09R 
       12.00         9.99        12.00        50.04        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-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        27.02        17.03        38.04 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       22.95        73.91         5.72        22.26        73.05        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79        29.26        16.80        14.96        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR 
       13.58        12.26         1.68         0.03        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        2.30         0.33         0.33         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         7.46         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-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.17         6.90         0.36         0.33         0.33         5.36 
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-A03M TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        61.35        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 
       69.83        58.95        44.42        32.78        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 
       76.77        65.10        26.24        62.04       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03       102.31        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       70.42        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       82.62        11.51        26.93       130.09        15.62        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      140.55        98.33         5.26        84.10       109.02        75.22 
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       133.22 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      107.21       125.16       108.36       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        93.90        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      118.59         2.76       104.28       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 
       50.96        98.76        98.66        89.00        99.62        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       71.05        93.83       166.42        20.25        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 
       38.17        39.39        40.54        33.30        38.96       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      281.29        11.90       275.87        50.70        65.52       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.28 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       282.90       169.51        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.46        18.35       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
       28.27        68.94        58.55        43.59        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       37.87        85.35       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        84.13        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 
       43.53        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        85.87        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       74.14        46.39        89.06        81.73        77.98        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS 
       38.01        29.98        13.91        78.28        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       79.00        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30         9.63        44.81        81.83        63.32        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       10.78        63.39        53.26        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-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-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       42.35        44.81         4.90        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
       72.56        37.74        30.28        55.63        37.55         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-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        97.48        25.08       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       122.83        33.99        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       72.07        53.98        28.14        26.14        38.60        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        23.51         9.63         5.26        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W 
        9.44        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
       12.92        12.46        12.49        12.33        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B 
       12.53        15.45        16.87        16.70         0.03        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 
       33.99        12.95        13.02        13.41        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        13.97        14.17        13.48        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        55.50        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        20.12        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-A1XF TCGA-D8-A1XG 
       23.90        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       21.83        14.50        19.92        17.69        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31        12.99        15.16        43.04        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-A27R 
       14.43        48.03        16.41        17.06         1.61        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        12.66        25.22        43.00        34.42        27.52 
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-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        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        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       69.96        23.24        19.43        21.04        23.87        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        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        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        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       35.77        25.84        18.94        28.27        34.95         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        3.02        11.15        45.01        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        21.27        47.64        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       39.09        38.37        41.72        40.50        20.12        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56        12.33         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY 
       18.90        13.25        16.57        28.77        25.94        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       19.96        25.91        22.09        34.03        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       59.57       216.76        79.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       32.75        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 
        2.63        16.08        15.68         7.46        19.53        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 
       58.62        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-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-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       64.21        86.96         0.26         9.93        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-XX-A899 
       20.68        19.27        13.84        17.26        17.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             160.9              282.9 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.790             28.885 
[1] "0.2 - 160.9 (24.8)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         9       11        0        1        57        37
  19Q LOSS WILD-TYPE      80       72        6        5       295       216
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           1         29          3          8        6
  19Q LOSS WILD-TYPE         1        126         24         57       14
                    vv
clus                 STAGE X
  19Q LOSS MUTATED         2
  19Q LOSS WILD-TYPE      11
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                 11                 72
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                57                295
  STAGE IIB                37                216
  STAGE III                 1                  1
  STAGE IIIA               29                126
  STAGE IIIB                3                 24
  STAGE IIIC                8                 57
  STAGE IV                  6                 14
  STAGE X                   2                 11
[1] 12  2
[1] TRUE
[1] "dimension of 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    40 103  16   5
  19Q LOSS WILD-TYPE 234 522 121  35
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               40                234
  T2              103                522
  T3               16                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
  19Q LOSS MUTATED    66  61  24  11
  19Q LOSS WILD-TYPE 440 297  95  66
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               66                440
  N1               61                297
  N2               24                 95
  N3               11                 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"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   131   6
  19Q LOSS WILD-TYPE 758  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    131    6
  19Q LOSS WILD-TYPE  758   16
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              131                758
  1                6                 16
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   161   3
  19Q LOSS WILD-TYPE 906   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    161    3
  19Q LOSS WILD-TYPE  906    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE              161                906
  MALE                  3                  9
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    66  88
  19Q LOSS WILD-TYPE 371 459
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     66   88
  19Q LOSS WILD-TYPE  371  459
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                66                371
  YES               88                459
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q LOSS MUTATED                            0                           144
  19Q LOSS WILD-TYPE                          1                           624
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q LOSS MUTATED                                5                   1
  19Q LOSS WILD-TYPE                            196                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q LOSS MUTATED                       0                                4
  19Q LOSS WILD-TYPE                     9                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  19Q LOSS MUTATED                    4              5
  19Q LOSS WILD-TYPE                 13             41
D76V9, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 144                624
  INFILTRATING LOBULAR CARCINOMA                  5                196
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 26
  MUCINOUS CARCINOMA                              4                 13
  OTHER, SPECIFY                                  5                 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"
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                          37    95
  19Q LOSS WILD-TYPE                       144   649
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                      37                144
  WHITE                                          95                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"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 131
  19Q LOSS WILD-TYPE  34 743
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  131
  19Q LOSS WILD-TYPE   34  743
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              131                743
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    76  16
  20P LOSS WILD-TYPE 841 132
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                92                973 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                132 
$`20P LOSS MUTATED`
TCGA-A7-A26E TCGA-A7-A26I TCGA-A8-A08F TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AO-A1KT 
       31.36        21.73        33.01        16.57        13.71        17.79 
TCGA-AQ-A54N TCGA-AR-A1AR TCGA-BH-A18H TCGA-E2-A2P5 TCGA-LL-A5YP TCGA-5T-A9QA 
        2.56        17.23        21.44        26.99        14.79         9.96 
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0YE TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CE 
       31.79        73.84        18.21        29.98        21.90        35.31 
TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A07L TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A0AB 
       21.17         1.02        32.05         9.99        31.00        17.03 
TCGA-AN-A0AM TCGA-AN-A0XW TCGA-AO-A0J6 TCGA-AQ-A04J TCGA-AR-A0TZ TCGA-AR-A0U3 
        0.16         5.59        37.48        26.93       107.24       134.14 
TCGA-AR-A24K TCGA-AR-A251 TCGA-AR-A252 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.89        99.62        93.30        11.90       233.62        18.77 
TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0X1 TCGA-B6-A1KN TCGA-B6-A400 TCGA-BH-A0AV 
       81.17       100.70       245.10       139.17         7.07        59.84 
TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BR TCGA-BH-A0DH TCGA-BH-A0E1 TCGA-BH-A18V 
       39.16        51.68        76.60        38.01        15.68        51.16 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FM TCGA-C8-A12M TCGA-C8-A134 TCGA-C8-A8HQ 
      114.15        33.17        45.63        11.77        12.59        12.49 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.12        20.09        19.40        27.58        21.83        14.50 
TCGA-D8-A1XQ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R TCGA-E2-A14N 
       16.41        14.14        16.04        13.05        10.09        47.15 
TCGA-E2-A14R TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1NC 
       38.60        23.34        20.71        34.92        36.82        39.55 
TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A22G TCGA-E9-A244 TCGA-EW-A1P4 TCGA-EW-A1P8 
       11.15        46.65        40.73         0.69        29.82         7.86 
TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2DF TCGA-JL-A3YX 
       55.00        22.09        17.49        17.52        70.85        11.57 
TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66O TCGA-OL-A6VO TCGA-PL-A8LX 
       22.39        36.36        20.38        17.36        28.21         0.16 
TCGA-S3-AA0Z TCGA-WT-AB44 
       20.68        29.03 

$`20P LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        38.30        23.61        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C 
       19.99        15.06        33.01        33.01        17.95         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       49.05        45.07        29.98        19.79        14.53        19.33 
TCGA-AO-A0JI TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL 
       50.24         5.65        32.91        19.20        98.33        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A1F5 
       57.27        73.35        81.63        54.05        32.58        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
        9.70        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       73.64        50.07        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU 
       13.22        24.95        29.23        25.05        14.50        40.08 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU 
       18.87        13.94        11.41        52.96       108.07       133.05 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD 
      131.67        48.46        47.61        11.44         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ 
       43.43        48.10        14.27        47.24        20.88        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        39.32        28.01        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       78.41       121.94        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS 
       99.12        24.79       114.81        92.48       107.93        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        98.99       107.93        56.81        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       118.45        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-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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        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        36.23        39.65        33.93        91.07        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CG 
       24.39        21.30        23.21        26.96        21.14        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-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
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-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        17.92        14.73        12.10        10.72 
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-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        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-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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 
      112.08        43.00        40.01        30.97        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
        9.99         9.99        12.00        50.04        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-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04        19.23        22.95        73.91         5.72        22.26 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       25.05        14.99        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       16.80        14.96        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-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-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-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         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         6.90         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         5.36 
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-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33        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        69.83        58.95        44.42        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        52.18        26.04        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        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        62.04        55.33        71.80       115.27       113.62 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03       102.31        98.27        82.68 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       70.42        60.56        53.88        40.57        20.45        97.08 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       61.87        82.62        11.51        24.79       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       83.87       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27       102.84       105.30        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        98.66        89.00        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       112.37       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       255.68        68.45       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       162.05       102.77       140.28        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      169.51        97.48       188.68        79.46        18.35        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       206.86       129.70        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 
       43.59       101.52        73.51       170.17        37.87        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       74.99        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 
       20.45        25.55        63.09        81.44        39.55        70.22 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       84.13        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       85.87        77.75        49.94        77.95        74.14        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       46.39        89.06        90.97        81.73        77.98        67.10 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 
       79.00        67.86        70.88        16.27         4.41        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        81.83        24.49        31.00        63.32 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        63.39        53.26        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        32.91         4.90        35.93        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-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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE 
       25.81        31.53        97.48        25.08       120.62        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.83        33.99        63.35        55.00        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.88        18.64        23.51         9.63         5.26        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
       12.56        12.16        13.51        12.59        12.92        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.49        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95        15.45        16.87        16.70         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.76        24.56        14.43        33.99        12.95        13.02 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        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        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP 
       53.00        14.01        18.97        20.09        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-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-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.73        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        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-A27T 
       48.03        16.41        13.48        17.06         1.61        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 
       12.66        25.22        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-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        33.17        75.98        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        69.34        18.51        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        25.05        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        22.29        34.16        36.20        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       41.62        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF 
       48.23        45.01        32.09        40.24         1.12         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       37.74        39.09        38.37        41.03        41.72        40.50 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        40.41        41.13        39.78        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 
       14.43        34.55        19.96        52.73        25.91        34.03 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       23.51        15.22        16.77        24.99        31.30        33.21 
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-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-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-LD-A66U 
       13.55        18.12         2.60        62.47        11.84        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        58.62        34.92 
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-A66P TCGA-OL-A6VQ TCGA-OL-A6VR 
       41.92        42.77        26.04        14.07        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-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 
       18.81        18.48        21.07        19.27        13.84        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 TCGA-XX-A89A 
       17.26        17.03         3.81        66.84        15.35        16.04 
TCGA-Z7-A8R6 
      107.05 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.16               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             245.1              282.9 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             22.24              28.77 
[1] "0.2 - 245.1 (22.2)" "0.0 - 282.9 (28.8)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         4        6        0        0        37        20
  20P LOSS WILD-TYPE      85       77        6        6       315       233
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0         15          2          6        3
  20P LOSS WILD-TYPE         2        140         25         59       17
                    vv
clus                 STAGE X
  20P LOSS MUTATED         0
  20P LOSS WILD-TYPE      13
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   4                 85
  STAGE IA                  6                 77
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                37                315
  STAGE IIB                20                233
  STAGE III                 0                  2
  STAGE IIIA               15                140
  STAGE IIIB                2                 25
  STAGE IIIC                6                 59
  STAGE IV                  3                 17
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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    17  65   8   3
  20P LOSS WILD-TYPE 257 560 129  37
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               17                257
  T2               65                560
  T3                8                129
  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
  20P LOSS MUTATED    42  31  11   7
  20P LOSS WILD-TYPE 464 327 108  70
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               42                464
  N1               31                327
  N2               11                108
  N3                7                 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"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    73   5
  20P LOSS WILD-TYPE 816  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     73    5
  20P LOSS WILD-TYPE  816   17
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               73                816
  1                5                 17
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    92   1
  20P LOSS WILD-TYPE 975  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     92    1
  20P LOSS WILD-TYPE  975   11
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               92                975
  MALE                  1                 11
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    30  55
  20P LOSS WILD-TYPE 407 492
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     30   55
  20P LOSS WILD-TYPE  407  492
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                30                407
  YES               55                492
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P LOSS MUTATED                            0                            76
  20P LOSS WILD-TYPE                          1                           692
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P LOSS MUTATED                                8                   2
  20P LOSS WILD-TYPE                            193                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P LOSS MUTATED                       0                                2
  20P LOSS WILD-TYPE                     9                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  20P LOSS MUTATED                    1              4
  20P LOSS WILD-TYPE                 16             42
D77V9, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  76                692
  INFILTRATING LOBULAR CARCINOMA                  8                193
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  4                 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"
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                          24    57
  20P LOSS WILD-TYPE                       157   687
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                      24                157
  WHITE                                          57                687
[1] 4 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  72
  20P LOSS WILD-TYPE  34 802
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   72
  20P LOSS WILD-TYPE   34  802
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               72                802
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    45  10
  20Q LOSS WILD-TYPE 872 138
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                55               1010 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                138 
$`20Q LOSS MUTATED`
TCGA-A7-A26E TCGA-A7-A26I TCGA-AC-A62X TCGA-AQ-A54N TCGA-AR-A1AR TCGA-E2-A2P5 
       31.36        21.73        13.71         2.56        17.23        26.99 
TCGA-LL-A5YP TCGA-A1-A0SK TCGA-A2-A3XU TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A6VW 
       14.79        31.79        29.98        35.31        35.67         9.37 
TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08O TCGA-A8-A0AB TCGA-AN-A0AR TCGA-AN-A0XW 
        1.02        43.00        31.00        17.03         0.33         5.59 
TCGA-AO-A03P TCGA-AO-A0J6 TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AR-A0U3 TCGA-AR-A24K 
       95.70        37.48        11.51        26.93       134.14        50.89 
TCGA-AR-A251 TCGA-AR-A252 TCGA-B6-A0RS TCGA-B6-A0X1 TCGA-B6-A400 TCGA-BH-A0AV 
       99.62        93.30       100.70       245.10         7.07        59.84 
TCGA-BH-A0BL TCGA-BH-A18V TCGA-BH-A1FC TCGA-C8-A12M TCGA-C8-A27B TCGA-C8-A8HQ 
       74.89        51.16       114.15        11.77        14.43        12.49 
TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-E2-A14N TCGA-E2-A15E TCGA-E9-A1NC 
       20.09        21.83        14.50        47.15        20.71        39.55 
TCGA-E9-A22G TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GM-A2DF 
       40.73        29.82         7.86        22.09        17.49        70.85 
TCGA-JL-A3YX TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66O TCGA-OL-A6VO TCGA-S3-AA0Z 
       11.57        22.39        36.36        17.36        28.21        20.68 
TCGA-WT-AB44 
       29.03 

$`20Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H 
       19.56       107.70        38.30        23.61        24.26        23.80 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U 
       22.32        11.28        11.97        11.05        53.06        29.03 
TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 
       19.99        15.06        33.01        33.01        33.01        17.95 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
        1.02        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O 
       14.53        19.33        50.24        17.79         5.65        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 
       19.20        98.33        66.15        57.27        73.35        81.63 
TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL 
       54.05        32.58        21.44        89.16         9.70        10.42 
TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG 
       21.14        14.79        50.79        16.47        73.64        50.07 
TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       15.68        52.96        75.02        85.35        13.22        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 
       29.23        25.05        14.50        40.08        18.87        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ 
       11.41        52.96       108.07       133.05       131.67        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE 
       47.61        11.44         9.96         8.52        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.10        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
      121.94        73.84        87.25       101.98        55.43       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS 
       99.12        24.79       114.81        92.48       107.93        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        98.99       107.93        56.81        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       118.45        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-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-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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.20        16.47        52.47        42.44        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        36.23        39.65        33.93        91.07 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
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-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.90        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G 
       29.79        31.73        20.19        25.15        29.56        23.74 
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-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-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-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        17.98        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        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-A07U 
       32.05         9.99        10.98         8.98         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-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-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
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-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        27.02        38.04        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72        22.26        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        25.05        14.99        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       24.79        29.26        16.80        14.96        11.44        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-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-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         7.46         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-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         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-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        69.83        58.95        44.42 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        21.40        52.18        26.04        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       65.10        26.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      113.62       108.72       106.78       108.03       102.31        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       82.68        70.42        60.56        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       97.08        61.87        82.62        24.79       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        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 
      133.22        83.87       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      103.86        97.68        96.00        86.07        93.90        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
      104.28       112.77        97.84       105.27       102.84       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 
       50.96        98.76        98.66        89.00        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.52       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      162.05       102.77       140.28        89.46       282.90       169.51 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.46        18.35        21.01       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      206.86       129.70        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 
      101.52        73.51       139.17       170.17        37.87        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       74.99        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        84.13        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 
       43.53        61.51        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        85.87        77.75        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        67.10        38.01        29.98        13.91        78.28 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        79.00        67.86        70.88 
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-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       81.83        24.49        31.00        63.32        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        63.39        53.26        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        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        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-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-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-A1FE TCGA-BH-A1FG 
       97.48        25.08       120.62        33.17        74.73       122.83 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       33.99        63.35        55.00        45.63        72.07        53.98 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       55.50        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        36.82        36.79        20.12        10.52       110.60 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.88        18.64        23.51         9.63         5.26        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.56        12.16        13.51        12.59        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.46        12.49        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95        15.45        16.87        16.70 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.76        24.56        33.99        12.95        13.02 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        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        55.50        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-A1JM 
       53.00        14.01        18.97        20.09        20.12        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-A1XL TCGA-D8-A1XM 
       12.39        17.16        15.22        14.73        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       55.30        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        43.04        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        48.03        16.41        13.48        17.06         1.61 
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        12.66        25.22        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-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 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       18.51        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       23.87        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        87.22        33.01        32.35        28.50        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       60.36        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        38.76        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       32.88        36.82        22.29        34.16        36.20        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       41.62        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        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 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       41.72        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 
        8.48        18.21        18.90        13.25        16.57        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-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       39.78        23.11        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-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       55.00        52.73        25.91        34.03        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       15.22        16.77        24.99        31.30        33.21         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-A3NW 
       85.15        86.96       115.69       106.06       101.62       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-LD-A66U TCGA-LD-A7W5 
       18.12         2.60        62.47        11.84        21.24         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       13.28        10.62        32.75        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-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       19.53        12.36        19.59        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX 
       36.30        58.52        31.99        58.62        34.92        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-A6VQ TCGA-OL-A6VR 
       41.92        42.77        26.04        14.07        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-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        21.07        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-XX-A899 
       17.39        17.26        17.03         3.81        66.84        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.33               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             245.1              282.9 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             26.99              28.27 
[1] "0.3 - 245.1 (27.0)" "0.0 - 282.9 (28.3)"
[1] "hr=" "1.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         3        2        0        0        26        14
  20Q LOSS WILD-TYPE      86       81        6        6       326       239
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          8          1          2        1
  20Q LOSS WILD-TYPE         2        147         26         63       19
                    vv
clus                 STAGE X
  20Q LOSS MUTATED         0
  20Q LOSS WILD-TYPE      13
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   3                 86
  STAGE IA                  2                 81
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                26                326
  STAGE IIB                14                239
  STAGE III                 0                  2
  STAGE IIIA                8                147
  STAGE IIIB                1                 26
  STAGE IIIC                2                 63
  STAGE IV                  1                 19
  STAGE X                   0                 13
[1] 12  2
[1] TRUE
[1] "dimension of 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    10  41   5   1
  20Q LOSS WILD-TYPE 264 584 132  39
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1               10                264
  T2               41                584
  T3                5                132
  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    29  20   5   3
  20Q LOSS WILD-TYPE 477 338 114  74
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               29                477
  N1               20                338
  N2                5                114
  N3                3                 74
[1] 4 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    46   2
  20Q LOSS WILD-TYPE 843  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     46    2
  20Q LOSS WILD-TYPE  843   20
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               46                843
  1                2                 20
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                    0    1
  20Q LOSS MUTATED     57    0
  20Q LOSS WILD-TYPE 1010   12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     57    0
  20Q LOSS WILD-TYPE 1010   12
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               57               1010
  MALE                  0                 12
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    22  30
  20Q LOSS WILD-TYPE 415 517
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     22   30
  20Q LOSS WILD-TYPE  415  517
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                22                415
  YES               30                517
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q LOSS MUTATED                            0                            42
  20Q LOSS WILD-TYPE                          1                           726
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q LOSS MUTATED                                7                   3
  20Q LOSS WILD-TYPE                            194                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q LOSS MUTATED                       0                                1
  20Q LOSS WILD-TYPE                     9                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  20Q LOSS MUTATED                    1              3
  20Q LOSS WILD-TYPE                 16             43
D78V9, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  42                726
  INFILTRATING LOBULAR CARCINOMA                  7                194
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 29
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  3                 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"
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                          17    30
  20Q LOSS WILD-TYPE                       164   714
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                      17                164
  WHITE                                          30                714
[1] 4 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  45
  20Q LOSS WILD-TYPE  35 829
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   45
  20Q LOSS WILD-TYPE   35  829
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO               45                829
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   151  26
  21Q LOSS WILD-TYPE 766 122
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               177                888 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                122 
$`21Q LOSS MUTATED`
TCGA-5L-AAT1 TCGA-A7-A26E TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09I 
       48.36        31.36        29.03        33.01        33.01        45.07 
TCGA-AQ-A0Y5 TCGA-E2-A1L8 TCGA-S3-AA17 TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SN 
        5.65        73.64        13.94       131.67        48.46        39.32 
TCGA-A2-A04T TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EU TCGA-A2-A0SU TCGA-A2-A0YJ 
       73.84       107.93        67.33        34.29        54.64        18.61 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XY TCGA-A2-A3Y0 
       23.77        23.47        17.36        42.44        35.93        50.83 
TCGA-A7-A0CJ TCGA-A7-A26G TCGA-A7-A4SD TCGA-A8-A06P TCGA-A8-A079 TCGA-A8-A08G 
       30.61        23.74        14.50        13.02         9.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09Q 
       12.00        37.05        31.00         9.99        12.00        25.02 
TCGA-A8-A09R TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A2BK TCGA-AC-A2BM 
        8.98        19.04        13.02        27.02        73.05        99.35 
TCGA-AC-A4ZE TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A04A TCGA-AN-A04C 
       29.26         8.22        20.19         1.12         2.96         1.78 
TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L 
        0.16         7.96         0.33         0.33         0.33        80.28 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD 
       95.70        68.75        21.40        52.18        20.32        72.00 
TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
      130.09       140.55       109.02       107.24       133.22        83.87 
TCGA-AR-A1AP TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 
       93.90        97.84       102.84       105.30        50.96        89.00 
TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LK TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0RP 
       93.30        93.83        54.21       129.57        65.52       102.77 
TCGA-B6-A0RS TCGA-B6-A0WW TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN 
      100.70        18.35       245.10        58.55        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0BG 
      170.17        68.12        62.93        59.84        51.68        61.51 
TCGA-BH-A0BP TCGA-BH-A0DE TCGA-BH-A0DP TCGA-BH-A0E9 TCGA-BH-A0H7 TCGA-BH-A0HU 
       75.48        77.98        15.65        81.83        23.08        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V 
       27.25        50.79        23.93        26.66        51.39        51.16 
TCGA-BH-A1FM TCGA-BH-A5J0 TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       45.63        23.51        12.66        12.66        12.66        12.66 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26W 
       12.46        12.49        10.92        12.03        12.95        12.53 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A145 TCGA-D8-A1J8 
       24.56        14.43        13.02        13.41        13.48        14.17 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JM TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.15        12.03        19.40        17.79        27.58        18.15 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       15.22        19.92        15.85        16.54        15.32         9.93 
TCGA-D8-A27M TCGA-D8-A27T TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C 
       13.48        13.08        12.26        34.42        46.59        40.11 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A1IH TCGA-E2-A1LL TCGA-E2-A56Z 
       20.71        18.21        12.92        33.73        43.04         8.28 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A1R0 
       38.76        34.16        36.56        41.62        18.94        28.27 
TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22G 
        6.12        45.01        32.09        21.27        34.45        40.73 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1IW 
       20.12        38.99         1.94        30.18         0.79        12.20 
TCGA-EW-A1J6 TCGA-EW-A2FS TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DL TCGA-GM-A4E0 
       28.77        52.73        33.21       109.87       115.69        72.03 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A5YM TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A6VQ 
        2.60        11.57        15.32        22.32        26.04        19.73 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
        0.16        18.81        18.48 

$`21Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 
       48.56        19.20        63.12        36.13        88.60        19.56 
TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
      107.70        38.30        23.61        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A07E 
       22.32        11.28        11.97        11.05        53.06        19.99 
TCGA-A8-A084 TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K 
       15.06        33.01        17.95         1.02        49.05        29.98 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AO-A0JI 
       16.57        19.79        14.53        19.33        13.71        50.24 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         2.56        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 
       21.44        89.16         9.70        10.42        21.14        14.79 
TCGA-E2-A15O TCGA-E2-A1BC TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 
       50.79        16.47        50.07        26.99        15.68        52.96 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       75.02        85.35        13.22        24.95        29.23        25.05 
TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 
       14.79        14.50        40.08        18.87        11.41        52.96 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      108.07       133.05        47.61        11.44         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-A0SQ TCGA-A2-A04N 
       13.68        31.79         7.96        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       18.02        78.41       121.94        87.25       101.98        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
      136.73        99.12        24.79       114.81        92.48       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
       77.19        75.25         5.19        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-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      118.45        79.76        74.40        72.00        35.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       61.94        24.72        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-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       18.21        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       48.46        31.73        60.72        22.45        20.25        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        52.47        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 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        47.31        50.37         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-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D 
       35.47        37.45        35.67        33.11        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        25.15        29.56        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       10.29        13.41        14.70        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
       10.42         8.75        13.02         1.02        17.98        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F 
       26.01         1.02        17.03        53.98        43.00        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-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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N 
       41.98        12.00         9.99        50.04        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        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72        22.26        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EH 
       25.05        14.99        15.48        23.24        24.79        16.80 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         0.03         1.32         2.30         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.23         0.33         0.62         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         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-A0FW 
        7.00         7.59         7.17         6.90         7.04         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         5.36         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-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       66.77        81.63        69.83        58.95        44.42        32.78 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        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        65.10        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       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      102.31        98.27        82.68        70.42        60.56        53.88 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        20.45        97.08        61.87        82.62        11.51 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TR 
       24.79        26.93        15.62        32.52        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       84.10        75.22        98.93        64.83        55.86        65.36 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       97.68        96.00        86.07        99.32        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        86.53        86.43        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       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 
      112.77       105.27        98.76        98.66        99.62        85.64 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       71.05       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
      143.38       281.29        11.90       275.87        50.70       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       263.28       162.05       140.28        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX 
      282.90       169.51        97.48       188.68        79.46        21.01 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KF 
      113.79       206.86       129.70        28.27        68.94       101.52 
TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
       73.51        37.87         7.07        85.35        74.99        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.55        39.16        70.22        84.13        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        85.87        77.75        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ 
       67.10        38.01        29.98        13.91        78.28         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        79.00        67.86        70.88        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 
       63.32        30.35        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 
        2.50        13.61        36.85        51.32         5.59        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        32.91         4.90        35.93 
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-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05         7.36        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-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        97.48        25.08       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       122.83        33.99        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       110.60        20.88        18.64         9.63         5.26 
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-A12P TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       11.77        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HG 
       13.51        12.59        12.59        12.92        12.33        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X 
       11.28         0.16        12.33        12.33        20.25        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95        15.45        16.87        16.70         0.03         9.76 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       33.99        12.95        12.49        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        13.97        14.17        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        55.50        15.78        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.12        20.09        20.38        21.01 
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-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       23.90        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-A1XU 
       17.69        55.30        16.41        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        43.04        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        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       17.06         1.61        10.09        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 
       21.67        16.18        12.66        25.22        43.00        27.52 
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-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        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        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       69.96        23.24        19.43        21.04        23.87        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        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        11.05        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II 
       28.50        37.25        77.65        37.41        70.36        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      106.75       102.61         8.75        34.55        43.56        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       22.29        36.20        39.55        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
        9.86        24.82        34.95         2.56         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       48.23        40.24         1.12        46.65         6.58        46.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       47.64        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A24A 
       41.03        41.72        40.50         0.69         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       12.33        29.72         9.47        38.07        32.91        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70        25.81        26.40        27.85 
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-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-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-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-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        17.52        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       31.30         7.40        59.57       216.76        79.10        83.34 
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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A5PV 
      110.50        38.20        43.73        69.30        66.38        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 
       18.12        62.47        11.84        21.24         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       10.62        32.75        17.06        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63        16.08        15.68         7.46        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VR TCGA-OL-A97C 
       42.77        17.36        14.07        28.21        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH 
       47.01        64.21        86.96         0.26         9.93        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       20.68        19.27        13.84        17.39        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        29.03        15.35        16.04       107.05 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.16               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             245.1              282.9 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            27.250             28.355 
[1] "0.2 - 245.1 (27.2)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED        10       12        0        0        50        51
  21Q LOSS WILD-TYPE      79       71        6        6       302       202
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         31          9          5        6
  21Q LOSS WILD-TYPE         1        124         18         60       14
                    vv
clus                 STAGE X
  21Q LOSS MUTATED         3
  21Q LOSS WILD-TYPE      10
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 12                 71
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                50                302
  STAGE IIB                51                202
  STAGE III                 1                  1
  STAGE IIIA               31                124
  STAGE IIIB                9                 18
  STAGE IIIC                5                 60
  STAGE IV                  6                 14
  STAGE X                   3                 10
[1] 12  2
[1] TRUE
[1] "dimension of 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    38 108  22  11
  21Q LOSS WILD-TYPE 236 517 115  29
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               38                236
  T2              108                517
  T3               22                115
  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    72  65  30   9
  21Q LOSS WILD-TYPE 434 293  89  68
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               72                434
  N1               65                293
  N2               30                 89
  N3                9                 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"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   147   8
  21Q LOSS WILD-TYPE 742  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    147    8
  21Q LOSS WILD-TYPE  742   14
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              147                742
  1                8                 14
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   179   0
  21Q LOSS WILD-TYPE 888  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    179    0
  21Q LOSS WILD-TYPE  888   12
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE              179                888
  MALE                  0                 12
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    79  89
  21Q LOSS WILD-TYPE 358 458
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     79   89
  21Q LOSS WILD-TYPE  358  458
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                79                358
  YES               89                458
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q LOSS MUTATED                            0                           143
  21Q LOSS WILD-TYPE                          1                           625
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q LOSS MUTATED                               21                   2
  21Q LOSS WILD-TYPE                            180                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q LOSS MUTATED                       2                                7
  21Q LOSS WILD-TYPE                     7                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  21Q LOSS MUTATED                    1              3
  21Q LOSS WILD-TYPE                 16             43
D79V9, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 143                625
  INFILTRATING LOBULAR CARCINOMA                 21                180
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 23
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                  3                 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"
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                          35   109
  21Q LOSS WILD-TYPE                       146   635
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                      35                146
  WHITE                                         109                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"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5 142
  21Q LOSS WILD-TYPE  34 732
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5  142
  21Q LOSS WILD-TYPE   34  732
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              142                732
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   410  70
  22Q LOSS WILD-TYPE 507  78
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               480                585 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                 78 
$`22Q LOSS MUTATED`
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A26I 
       63.12        36.13        88.60       107.70        31.36        21.73 
TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 
       11.28        11.97        53.06        29.03        19.99        15.06 
TCGA-A8-A08S TCGA-A8-A09C TCGA-AC-A5XS TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       33.01         1.02        19.33         2.56        32.91        19.20 
TCGA-AR-A1AM TCGA-AR-A1AR TCGA-BH-A0B6 TCGA-BH-A18H TCGA-BH-A1F5 TCGA-C8-A1HL 
       98.33        17.23        81.63        21.44        89.16        10.42 
TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-EW-A1P3 TCGA-LL-A442 
       21.14        50.79        73.64        26.99        52.96        29.23 
TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SD TCGA-A1-A0SG 
      108.07       133.05       131.67        48.46        14.37        14.27 
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       13.68        39.32        28.01       143.15        18.02        78.41 
TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79        92.48       107.93        77.19         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ET 
      107.93        67.33        25.22       134.40        80.28        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       34.29        31.82        61.94        54.64        27.12        50.43 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE 
       49.84        20.52        18.90        20.75        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G0 
       50.47        21.90        21.67        23.77        17.36        20.25 
TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 
       42.44        33.93        91.07        29.98        50.37        50.83 
TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.30        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26J 
       35.67        33.11        31.73        20.19        29.56        20.61 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW 
       13.74        14.50        21.17        17.92        14.73         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02         1.02        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I 
        1.02        17.03        53.98        43.00        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A08G 
       12.00        32.05         8.98         9.99        36.95        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A09B 
       12.00        37.05        31.00        40.01        12.00        12.00 
TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A4 
       50.04         1.02         8.98        19.04         0.99        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK 
       21.04         0.99        27.02        17.03        73.91        73.05 
TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP 
       90.71        26.04        33.04        32.45        16.31        22.19 
TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV 
       25.05        15.48        16.80        14.96        17.42        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A049 
       12.26         1.68         8.22        20.19         0.23         0.62 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FW 
        9.96         7.36         6.44         5.65         7.00         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33        80.28        66.77        95.70        21.40        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JG 
       22.36        53.03        21.53        50.70        72.00        26.24 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AR-A0TR 
      102.31        70.42        97.08        61.87        11.51         5.26 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 
      109.02        98.93        55.86       107.24        65.36        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ 
      134.14       125.16       101.00        96.00        93.90        99.32 
TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24O 
       61.28        33.73       160.90        50.89        94.22       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
        2.76       112.77        97.84        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO 
       89.00        93.30        71.05        93.83        54.21        39.39 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IN TCGA-B6-A0IO 
       33.30        38.96       146.50       112.37        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RO 
      140.88       255.68        68.45        81.17       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A3ZX 
      102.77        18.35        21.01       113.79       139.17        37.87 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY 
       68.12        18.84       103.63        71.15        62.93        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       81.44        39.55        39.16        70.22        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT 
       37.22        43.53        21.70        74.89        76.60        77.75 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DQ 
       49.94        74.14        89.06        90.97        38.01         3.22 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 
        4.41         9.63        24.49        30.35        10.78        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
       41.00        52.96        26.50        36.85        12.89        27.25 
TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I 
       23.93        42.35        44.81        23.05        32.91        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18T TCGA-BH-A18V 
       20.12        90.84        26.66        72.56         7.36        51.16 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F8 
      113.82        82.85        42.28        49.58        17.69        25.08 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A204 
      114.15        33.17        55.00        45.63        72.07        83.31 
TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12M 
      130.16        10.52        18.64        23.51         9.63        11.77 
TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK 
       12.66        48.53        12.59        12.49        11.28        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A8HP 
       12.33        12.95        15.45        16.70        24.56        13.02 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 
       19.46        56.81        20.88        14.17        13.48        14.17 
TCGA-D8-A1JB TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       55.50        53.00        20.09        19.40        20.38        21.01 
TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XK 
       18.58        23.90        27.58        18.15        17.16        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 
       17.69        55.30        15.85        16.64        12.99        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27T 
        9.93        14.24        14.14        14.43        16.41        13.08 
TCGA-D8-A3Z5 TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A 
       33.37        25.22        43.00        34.42        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       40.11        28.87        44.68        38.24        38.60        75.98 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A159 
       34.26        32.02        18.51        63.62        23.24        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       55.63        11.05        19.56        51.39        76.57        87.22 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       32.35        37.25        37.41        33.73        33.70        28.44 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A56Z 
        3.88        22.19        60.99        28.90         8.75         8.28 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 
       34.92        38.76        34.29        17.69        34.82        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       34.16        36.20        36.56        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 
       25.84        18.94         9.86        34.95         2.56        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       45.01        32.09        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       21.27        47.64        37.74        39.09        41.03        41.72 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       24.56        38.07        30.44        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 
       25.81        27.85        39.72        18.90        13.25        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA 
       22.82        29.85        23.11        18.48         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA 
        6.15        19.96        25.91        17.52        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       24.99        31.30        33.21       216.76        79.10        83.34 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-HN-A2NL 
       86.96       115.69        38.20        66.38        72.03         2.60 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YN TCGA-LL-A5YO 
       11.84        11.57        21.24         7.10        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW 
       22.26        12.36        27.91        58.52        34.92        36.36 
TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC 
       22.32        41.92        42.77        28.21        19.73        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       64.21        86.96         0.16         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A89A 
       21.07        19.27        17.03        66.84        29.03        16.04 

$`22Q LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A7-A13G 
       48.56        48.36        19.20        19.56        38.30        23.61 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A5ZX TCGA-A8-A08F TCGA-A8-A091 
       24.26        23.80        22.32        11.05        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 
       17.95        49.05        45.07        29.98        16.57        19.79 
TCGA-AC-A5EI TCGA-AC-A62X TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AR-A2LL 
       14.53        13.71        50.24        17.79         5.65        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A8FY TCGA-E2-A158 
       57.27        73.35        54.05        32.58         9.70        14.79 
TCGA-E2-A1BC TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       16.47        50.07        15.68        75.02        85.35        13.22 
TCGA-LL-A440 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 TCGA-OL-A5RU TCGA-S3-AA12 
       24.95        25.05        14.79        14.50        40.08        18.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA 
       13.94        11.41        52.96        47.61        11.44         9.96 
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
        8.52        43.43        48.10        47.24        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
        7.96        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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25C 
       60.72        22.45        19.20        16.47        52.47        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV 
       18.15       105.34        10.59        36.23        39.65        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 
       56.28        47.31        35.93         7.30        24.39        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26G 
       26.96        21.14        37.45        29.79        25.15        23.74 
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-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A079 
       12.10        10.72        10.29        10.42        13.02         9.01 
TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       18.97         9.99        10.98         7.99        24.99        45.07 
TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L 
       18.05        13.02         0.99        38.01        28.96         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A095 
       31.00         0.99       112.08        43.00        30.97        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09X 
        9.99         9.99        33.07        25.02        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
       12.00        19.04        38.04        19.23        22.95         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK 
       22.26        99.35        40.57        86.66        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QQ 
       74.14        19.33        14.66         6.48        14.83        24.13 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A62V TCGA-AC-A6IW 
       14.99        23.24        24.79        29.26        11.44        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         7.46         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 
        6.90         7.04         0.33         0.33         5.36         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 
       69.83        58.95        44.42        32.78        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A0JL 
       37.48        50.86        76.77        65.10        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27       113.62       108.72       106.78       108.03 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        60.56        53.88        40.57        20.45 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       82.62        24.79        26.93       130.09        15.62        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U1 
      140.55        98.33        84.10        75.22        64.83       133.22 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AS 
      107.21       108.36       103.86        97.68        86.07        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Q 
       94.29        86.53        86.43       120.33        99.78       104.28 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE 
      105.27       102.84       105.30        99.62        85.64       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QQ 
       20.25        86.53        63.62        38.17        40.54        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
       50.70        65.52       233.62        18.77       127.33       129.07 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      212.25       234.28        78.02       140.28       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ 
      282.90       169.51        97.48       188.68        79.46       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      101.52        73.51       170.17         7.07        85.35        74.99 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       59.84        20.45        63.09        32.02        18.21        61.51 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW 
       61.68        72.23        75.48        74.14        85.87        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       41.75        46.39        81.73        77.98        67.10        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        78.28        15.65         2.56        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       70.88        16.27        15.68        14.30        44.81        81.83 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        63.32        15.16        63.39        53.26        24.56 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY 
       20.38         5.85         2.50        13.61        51.32        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
        5.59        24.95         4.90        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV 
       37.55        66.05        51.39        69.93        91.99        12.00 
TCGA-BH-A1EW TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FE 
       55.69        25.81        31.53        97.48       120.62        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
      122.83        33.99        63.35        53.98        55.50        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        36.82        36.79        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      110.60        20.88         5.26        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
       11.93        11.77        12.66        11.77        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        12.56        12.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
       12.92        12.46        12.33        10.92        11.34         0.16 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 
       12.33        20.25        12.53        12.36        12.95        16.87 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        0.03         9.76        14.43        33.99        12.95        12.49 
TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1J9 
       13.41        13.25        20.58        13.97        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 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-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       18.97        20.12        20.09        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       17.79        16.73        25.74        12.39        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW 
       21.83        19.92        16.41        16.31        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       16.54        15.32        17.42        16.04        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       48.03        13.48        17.06         1.61        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A108 
       12.26        18.51        21.67        16.18        12.66        27.52 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U 
       37.51        28.44        47.15        40.96        33.17        43.33 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       31.96        69.34        69.96        19.43        21.04        23.87 
TCGA-E2-A15D TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S 
       17.29        53.92         9.04        20.58        56.94        14.07 
TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IK 
       53.62        33.01        28.50        77.65        70.36        59.18 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        60.36        19.66        24.59        75.81 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      106.75       102.61        43.04        34.55        43.56        30.61 
TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 
       32.88        22.29        39.55        24.82        28.27         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        3.02        48.23        46.59        34.45        32.05        42.25 
TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
       38.37        40.73        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ 
       30.18        23.90        26.40        12.20         8.48        18.21 
TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        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-A2DF TCGA-GM-A2DH 
       23.51         7.40       109.87        59.57        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XL 
       85.15       106.06       101.62       110.50        43.73        69.30 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       13.55        18.12        62.47        13.28        10.62        32.75 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       17.06        15.32         2.63        16.08        15.68         7.46 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.53        19.59        17.49        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       31.99        58.62        28.87        24.72        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VR 
       23.47        65.62        26.04        17.36        14.07        40.11 
TCGA-OL-A97C TCGA-PL-A8LY TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        8.91         0.26        20.68        13.84        17.39        17.26 
TCGA-UU-A93S TCGA-XX-A899 TCGA-Z7-A8R6 
        3.81        15.35       107.05 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.16               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            263.28             282.90 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            28.885             26.930 
[1] "0.2 - 263.3 (28.9)" "0.0 - 282.9 (26.9)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED        36       36        1        2       150       122
  22Q LOSS WILD-TYPE      53       47        5        4       202       131
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         70         10         35        8
  22Q LOSS WILD-TYPE         1         85         17         30       12
                    vv
clus                 STAGE X
  22Q LOSS MUTATED         7
  22Q LOSS WILD-TYPE       6
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  36                 53
  STAGE IA                 36                 47
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA               150                202
  STAGE IIB               122                131
  STAGE III                 1                  1
  STAGE IIIA               70                 85
  STAGE IIIB               10                 17
  STAGE IIIC               35                 30
  STAGE IV                  8                 12
  STAGE X                   7                  6
[1] 12  2
[1] TRUE
[1] "dimension of 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   115 294  54  17
  22Q LOSS WILD-TYPE 159 331  83  23
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1              115                159
  T2              294                331
  T3               54                 83
  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   218 163  55  41
  22Q LOSS WILD-TYPE 288 195  64  36
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0              218                288
  N1              163                195
  N2               55                 64
  N3               41                 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"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   403   9
  22Q LOSS WILD-TYPE 486  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    403    9
  22Q LOSS WILD-TYPE  486   13
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              403                486
  1                9                 13
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   475   7
  22Q LOSS WILD-TYPE 592   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    475    7
  22Q LOSS WILD-TYPE  592    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              475                592
  MALE                  7                  5
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   176 267
  22Q LOSS WILD-TYPE 261 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    176  267
  22Q LOSS WILD-TYPE  261  280
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               176                261
  YES              267                280
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q LOSS MUTATED                            0                           357
  22Q LOSS WILD-TYPE                          1                           411
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q LOSS MUTATED                               88                   2
  22Q LOSS WILD-TYPE                            113                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q LOSS MUTATED                       3                               19
  22Q LOSS WILD-TYPE                     6                               11
                    vv
clus                 MUCINOUS CARCINOMA OTHER, SPECIFY
  22Q LOSS MUTATED                    1             11
  22Q LOSS WILD-TYPE                 16             35
D80V9, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 357                411
  INFILTRATING LOBULAR CARCINOMA                 88                113
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)               19                 11
  MUCINOUS CARCINOMA                              1                 16
  OTHER, SPECIFY                                 11                 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"
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                          85   333
  22Q LOSS WILD-TYPE                        96   411
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                      85                 96
  WHITE                                         333                411
[1] 4 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    16 386
  22Q LOSS WILD-TYPE  23 488
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16  386
  22Q LOSS WILD-TYPE   23  488
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   16                 23
  NOT HISPANIC OR LATINO              386                488
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED   167  23
  XP LOSS WILD-TYPE 750 125
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              190               875 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23               125 
$`XP LOSS MUTATED`
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A084 TCGA-AO-A0JI 
       22.32        11.28        53.06        29.03        15.06        50.24 
TCGA-AQ-A54N TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1L8 TCGA-3C-AAAU TCGA-A1-A0SH 
        2.56        10.42        14.79        73.64       133.05        47.24 
TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CS 
       31.79       121.94        73.84        87.25        24.79        77.19 
TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO 
       75.25       107.93        67.33        34.55        25.22        80.28 
TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CJ 
       27.12        17.52        91.07        21.90        35.31        30.61 
TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW 
       10.59        14.93        14.50        17.92        14.73         9.37 
TCGA-A7-A6VY TCGA-A8-A06Y TCGA-A8-A085 TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A099 
        8.75        26.01        36.95         9.99        31.00         9.99 
TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AC-A4ZE 
        1.02         0.99        17.03        38.04        99.35        29.26 
TCGA-AC-A5EH TCGA-AC-A7VB TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR 
       16.80         8.22         2.96         7.36         0.16         0.33 
TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XT TCGA-AN-A0XU 
        6.44         7.96         0.33         5.36         0.33         0.33 
TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA TCGA-AO-A0JE 
       68.75        32.78        21.40        52.18        21.53        76.77 
TCGA-AO-A124 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AR-A0TV 
      115.27        60.56        61.87        82.62        15.62        75.22 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       55.86       107.24       133.22       134.14       107.21       125.16 
TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       33.73       104.28       112.77        99.62        85.64        93.83 
TCGA-AR-A2LO TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG 
       39.39        65.52       146.50        18.77       140.88        68.45 
TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0AV 
       81.17       282.90        79.46        21.01       139.17        59.84 
TCGA-BH-A0B0 TCGA-BH-A0BW TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DX 
       81.44        77.95        67.10        38.01        78.28        70.88 
TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0W3 
        9.63        63.32        10.78        52.96        51.32        23.93 
TCGA-BH-A0WA TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM 
       23.05       113.82        17.69        25.08        33.17        45.63 
TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A1HF 
       10.52        18.64        12.66        12.66        12.92        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A278 
       11.34         0.16        20.25        12.53        16.70         9.76 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J9 
       12.49        13.41        19.46        56.81        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X9 
       16.50        55.50        18.97        19.40        21.01        23.90 
TCGA-D8-A1XA TCGA-D8-A1XO TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R TCGA-D8-A27T 
       27.58        55.30        16.04        13.05        10.09        13.08 
TCGA-E2-A14P TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A15H TCGA-E2-A15P 
       40.96        69.34        69.96        21.04        12.92        19.56 
TCGA-E2-A15S TCGA-E2-A1IE TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A576 
       14.07        77.65        60.36        24.59       106.75        34.29 
TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NH TCGA-E9-A1R4 
       32.88        34.16        36.56        39.55        18.94         6.12 
TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A3HO TCGA-E9-A5UO TCGA-EW-A1J1 
       21.27        40.73        38.99        38.07        25.81        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A6SB 
       28.77        22.82        40.41        18.90        13.94        24.99 
TCGA-EW-A6SD TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LQ-A4E4 
       33.21        72.10         2.60        11.57        16.08        27.91 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DC TCGA-PE-A5DD 
       36.36        22.32        20.38        23.47        47.01        64.21 
TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
        0.16        21.07        17.39        16.04 

$`XP LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A08F 
       23.80        21.73        11.97        11.05        19.99        33.01 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
       33.01        33.01        17.95         1.02        49.05        45.07 
TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       29.98        16.57        19.79        14.53        19.33        13.71 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         5.65        32.91        19.20        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC 
       21.44        89.16         9.70        21.14        50.79        16.47 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        48.46        47.61        11.44         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ 
       14.37        43.43        48.10        14.27        20.88        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        39.32        28.01        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       78.41       101.98        55.43       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D2 
       92.48       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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.20        16.47        52.47        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        36.23        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        56.28        47.31        35.93        50.37        50.83 
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-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-A13H TCGA-A7-A26G TCGA-A7-A26J 
       31.73        20.19        25.15        29.56        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE 
       11.34        10.29        13.41        14.70        13.74        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P 
       12.10        10.72        10.29        10.42        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
        1.02        17.98        31.00         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        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-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
        9.99        45.07        18.05        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 
      112.08        43.00        40.01        30.97        41.98        12.00 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
        9.99        12.00        50.04        33.07        25.02         8.98 
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-A0A9 TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       21.04         0.99        27.02        19.23        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72        22.26        73.05        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       24.13        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         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-A04C 
        0.33         0.33         0.23         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF 
        1.71         9.96         7.46         0.33         0.33         5.65 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW 
        7.00         7.59         7.17         6.90         7.04         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 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-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-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        95.70        69.83        58.95        44.42 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB 
       26.04        37.48        20.32        22.36        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        72.00        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80       113.62       108.72       106.78       108.03       102.31 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        82.68        70.42        53.88        40.57        20.45 
TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 
       97.08        11.51        24.79        26.93       130.09        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
      140.55        98.33         5.26        84.10       109.02        98.93 
TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       64.83        65.36        83.87       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       97.68        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       94.29        61.28        86.53        86.43       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S 
       94.22       120.33        99.78       118.59         2.76        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27       102.84       105.30        50.96        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       89.00        93.30        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       54.21        63.62        38.17        40.54        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        11.90       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
      129.57        50.70       112.37       233.62       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      165.76       129.07       255.68       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.28       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ 
      169.51        97.48       188.68        18.35       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.55        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
      101.52        73.51       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       74.99        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       20.45        25.55        63.09        39.55        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ 
       74.14        76.60        85.87        77.75        49.94        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        46.39        89.06        90.97        81.73        77.98 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       29.98        13.91        15.65         3.22         2.56        79.00 
TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       67.86        16.27         4.41        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 
       81.83        24.49        31.00        30.35        15.16        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        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-A0HX 
        5.85         2.50        13.61        36.85        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
       50.79         5.59        24.95        42.35        44.81        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        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-A1ET TCGA-BH-A1EU 
       51.39        51.16        69.93        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       12.00        55.69        49.58        25.81        31.53        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62       114.15        74.73       122.83        33.99        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        72.07        53.98        55.50        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        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       20.12       110.60        20.88        23.51         9.63         5.26 
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-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       12.66        11.77        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.56        12.16        13.51        12.59        12.59        12.46 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       12.49        12.33        11.28        12.03        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
       12.33        12.36        12.95        15.45        16.87         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-D8-A13Z 
       24.56        14.43        33.99        12.95        13.02        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 
       13.25        20.58        13.97        14.17        13.48        14.17 
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        53.00        14.01 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        20.12        20.09        20.38        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB 
       14.70        18.58        17.79        16.73        25.74        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-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        43.04        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I 
        9.93        14.24        14.14        17.42        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V 
       48.03        16.41        13.48        17.06         1.61        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        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        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-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       32.02        31.96        18.51        63.62        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        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        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       11.05        56.94        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG 
       33.01        32.35        28.50        37.25        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       60.99        11.08        54.18        19.66        75.81        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        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 
       30.61        34.92        38.76        17.69        34.82        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       22.29        36.20        41.62        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        24.82        28.27        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12         0.69         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.33        29.72         9.47        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70         0.79        26.40        27.85 
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-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       25.94        29.95        29.85        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08         7.86        19.99         6.15 
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        17.52        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       15.22        16.77        31.30         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        79.10        83.34        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       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        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       11.84        21.24         7.10        13.28        10.62        32.75 
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-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68         7.46        19.53        12.36        19.59        17.49 
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-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       34.92        28.87        24.72        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        18.81 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 TCGA-UL-AAZ6 
       18.48        20.68        19.27        13.84        17.26        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
        3.81        66.84        29.03        15.35       107.05 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.16              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           282.90            281.29 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            25.91             28.44 
[1] "0.2 - 282.9 (25.9)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED        14       17        0        1        68        46
  XP LOSS WILD-TYPE      75       66        6        5       284       207
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  XP LOSS MUTATED           0         25          5          7        5       2
  XP LOSS WILD-TYPE         2        130         22         58       15      11
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                17                66
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               68               284
  STAGE IIB               46               207
  STAGE III                0                 2
  STAGE IIIA              25               130
  STAGE IIIB               5                22
  STAGE IIIC               7                58
  STAGE IV                 5                15
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    46 122  15   8
  XP LOSS WILD-TYPE 228 503 122  32
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              46               228
  T2             122               503
  T3              15               122
  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    93  64  22  11
  XP LOSS WILD-TYPE 413 294  97  66
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              93               413
  N1              64               294
  N2              22                97
  N3              11                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"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   165   6
  XP LOSS WILD-TYPE 724  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    165    6
  XP LOSS WILD-TYPE  724   16
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             165               724
  1               6                16
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   189   3
  XP LOSS WILD-TYPE 878   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    189    3
  XP LOSS WILD-TYPE  878    9
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE             189               878
  MALE                 3                 9
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    81  97
  XP LOSS WILD-TYPE 356 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     81   97
  XP LOSS WILD-TYPE  356  450
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               81               356
  YES              97               450
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP LOSS MUTATED                            0                           154
  XP LOSS WILD-TYPE                          1                           614
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP LOSS MUTATED                               21                   0
  XP LOSS WILD-TYPE                            180                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP LOSS MUTATED                       0                                6
  XP LOSS WILD-TYPE                     9                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  XP LOSS MUTATED                    3              7
  XP LOSS WILD-TYPE                 14             39
D81V9, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                154               614
  INFILTRATING LOBULAR CARCINOMA                21               180
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                24
  MUCINOUS CARCINOMA                             3                14
  OTHER, SPECIFY                                 7                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"
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                          42   116
  XP LOSS WILD-TYPE                       139   628
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                     42               139
  WHITE                                        116               628
[1] 4 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     7 156
  XP LOSS WILD-TYPE  32 718
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      7  156
  XP LOSS WILD-TYPE   32  718
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             156               718
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   163  24
  XQ LOSS WILD-TYPE 754 124
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              187               878 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               24               124 
$`XQ LOSS MUTATED`
TCGA-A7-A3J1 TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A084 TCGA-AO-A0JI TCGA-AQ-A54N 
       11.28        53.06        29.03        15.06        50.24         2.56 
TCGA-AR-A2LR TCGA-C8-A1HL TCGA-E2-A158 TCGA-E2-A1L8 TCGA-3C-AAAU TCGA-3C-AALI 
       57.27        10.42        14.79        73.64       133.05       131.67 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CT 
       47.24        31.79       121.94        87.25        77.19        75.25 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV 
      107.93        67.33        34.55        25.22        80.28        27.12 
TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A3Y0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CJ 
       17.52        91.07        50.83        21.90        35.31        30.61 
TCGA-A7-A0DA TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW 
       35.67        10.59        14.93        17.92        14.73         9.37 
TCGA-A7-A6VY TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A085 TCGA-A8-A08I TCGA-A8-A08L 
        8.75        26.01        17.03        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-A4ZE TCGA-AC-A5EH TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A0AJ 
       29.26        16.80         8.22         1.12         0.23         9.96 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        7.36         0.16         0.33         0.33         6.44         7.96 
TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J3 
        0.33         5.36         0.33         0.33        68.75        21.40 
TCGA-AO-A0JA TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A1KQ TCGA-AQ-A1H2 
       21.53        76.77        62.04       115.27        61.87        15.62 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
        5.26        75.22        55.86       107.24        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A251 TCGA-AR-A255 
      107.21       125.16        33.73       160.90        99.62        71.05 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IQ 
       93.83        39.39        65.52       146.50        18.77       140.88 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0B0 TCGA-BH-A0BR 
       68.45        81.17        21.01       139.17        81.44        76.60 
TCGA-BH-A0BV TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0GZ TCGA-BH-A0HA 
       49.94        67.10        38.01        70.88        10.78        52.96 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 
       12.89        51.32        23.93       113.82        17.69        25.08 
TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12Q TCGA-C8-A12X 
       33.17        45.63        10.52        18.64        12.66        12.66 
TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.92        10.92         0.16        12.33        20.25        12.53 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J9 
       12.49        13.41        19.46        56.81        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       16.50        55.50        18.97        20.09        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XO TCGA-D8-A1Y3 
       21.01        23.90        27.58        21.83        55.30        14.14 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A14P TCGA-E2-A152 TCGA-E2-A155 
       16.04        13.05        13.08        40.96        69.96        21.04 
TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A1IE TCGA-E2-A1L7 
       12.92         9.04        19.56        14.07        77.65        60.36 
TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
      106.75        34.29        32.88        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1R4 TCGA-E9-A1RG TCGA-E9-A22G 
       39.55        35.24        18.94         6.12        21.27        40.73 
TCGA-E9-A247 TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OZ 
       38.99        25.81        18.90        28.77        22.82        40.41 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A6SD TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX 
       18.90        13.94        33.21        72.10         2.60        11.57 
TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ 
       16.08        12.36        27.91        58.62        36.36        22.32 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-WT-AB44 
       47.01        64.21         0.16        21.07        17.39        29.03 
TCGA-XX-A89A 
       16.04 

$`XQ LOSS WILD-TYPE`
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ 
       48.56        48.36        19.20        63.12        36.13        88.60 
TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F 
       19.56       107.70        38.30        23.61        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A426 TCGA-A7-A5ZX TCGA-A8-A07E 
       23.80        21.73        22.32        11.97        11.05        19.99 
TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       33.01        33.01        33.01        17.95         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS 
       45.07        29.98        16.57        19.79        14.53        19.33 
TCGA-AC-A62X TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM 
       13.71        17.79         5.65        32.91        19.20        98.33 
TCGA-AR-A1AR TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0EA 
       17.23        66.15        73.35        81.63        54.05        32.58 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A1BC 
       21.44        89.16         9.70        21.14        50.79        16.47 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-GM-A2DO 
       50.07        26.99        15.68        52.96        75.02        85.35 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YP TCGA-LL-A740 
       13.22        24.95        29.23        25.05        14.79        14.50 
TCGA-OL-A5RU TCGA-S3-AA12 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 
       40.08        18.87        13.94        11.41        52.96       108.07 
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD 
       48.46        47.61        11.44         9.96         8.52        14.37 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       43.43        48.10        14.27        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       73.84       101.98        55.43       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
      114.81        92.48       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       118.45        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-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C 
       20.25        19.20        16.47        52.47        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        36.23        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
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-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D 
       34.29        35.47        37.45        33.11        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IY 
       20.19        25.15        29.56        23.74        20.61        11.34 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       10.29        13.41        14.70        13.74        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P 
       12.10        10.72        10.29        10.42        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
        1.02        17.98        31.00         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        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-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       19.96        37.05        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        30.97        41.98        12.00         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       50.04        33.07        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-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        27.02        19.23        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       22.26        73.05        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU 
       25.05        14.99        15.48        23.24        24.79        14.96 
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-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         7.46 
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         6.90 
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        69.83 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        44.42        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 
       65.10        26.24        55.33        71.80       113.62       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03       102.31        98.27        82.68        70.42 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       60.56        53.88        40.57        20.45        97.08        82.62 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AR-A0TP 
       11.51        24.79        26.93       130.09        32.52       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 
       98.33        84.10       109.02        98.93        64.83        65.36 
TCGA-AR-A0U1 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
      133.22       108.36       101.00       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.53        86.43        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      102.84       105.30        50.96        98.76        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       93.30        85.64       166.42        20.25        86.53        54.21 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       63.62        38.17        40.54        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        11.90       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       50.70       112.37       233.62       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      129.07       255.68       212.25       234.28        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.28       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
      169.51        97.48       188.68        79.46        18.35       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.55 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       43.59       101.52        73.51       170.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
       85.35        74.99        68.12        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 
       62.93        59.84        20.45        25.55        63.09        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       72.23        75.48        74.14        85.87        77.75        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       74.14        41.75        46.39        89.06        90.97        81.73 
TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       77.98        29.98        13.91        78.28        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        2.56        79.00        67.86        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        81.83        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       63.32        30.35        15.16        63.39        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       23.08        41.00        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-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05        32.91         4.90        35.93 
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-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       69.93        91.99        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        25.81        31.53        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       122.83        33.99        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       53.98        55.50        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        36.82        36.79        20.12       110.60 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        23.51         9.63         5.26        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-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56        12.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       13.51        12.59        12.59        12.46        12.49        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X 
       11.34        11.28        12.03        12.33        12.95        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95        15.45        16.87        16.70         0.03         9.76 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-D8-A13Z 
       24.56        14.43        33.99        12.95        13.02        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 
       13.25        20.58        13.97        14.17        13.48        14.17 
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        53.00        14.01 
TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.12        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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       15.22        14.73        14.50        19.92        17.69        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.54        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        14.43        48.03        16.41        13.48        17.06 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        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        12.66        25.22        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-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 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 
       18.51        63.62        23.24        19.43        23.87        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-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A15T 
       55.63        53.92        20.58        11.05        56.94        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       37.25        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK 
       19.66        24.59        75.81        28.90       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1ND 
       38.76        17.69        34.82        36.82        22.29        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.03        41.72        40.50        20.12         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        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       18.21        13.25        16.57        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        19.99         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-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        17.52        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       83.34        70.85        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       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        62.47        11.84        21.24 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM 
        7.10        13.28        10.62        32.75        17.06        15.32 
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-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.53        19.59        17.49        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       58.52        31.99        34.92        28.87        24.72        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-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z 
       86.96         0.26         9.93        18.81        18.48        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       19.27        13.84        17.26        17.03         3.81        66.84 
TCGA-XX-A899 TCGA-Z7-A8R6 
       15.35       107.05 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.16              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            160.9             282.9 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           25.220            28.685 
[1] "0.2 - 160.9 (25.2)" "0.0 - 282.9 (28.7)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED        14       15        0        0        64        53
  XQ LOSS WILD-TYPE      75       68        6        6       288       200
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  XQ LOSS MUTATED           0         23          4          7        5       2
  XQ LOSS WILD-TYPE         2        132         23         58       15      11
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                15                68
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               64               288
  STAGE IIB               53               200
  STAGE III                0                 2
  STAGE IIIA              23               132
  STAGE IIIB               4                23
  STAGE IIIC               7                58
  STAGE IV                 5                15
  STAGE X                  2                11
[1] 12  2
[1] TRUE
[1] "dimension of 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    40 123  17   8
  XQ LOSS WILD-TYPE 234 502 120  32
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              40               234
  T2             123               502
  T3              17               120
  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    89  69  19  10
  XQ LOSS WILD-TYPE 417 289 100  67
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              89               417
  N1              69               289
  N2              19               100
  N3              10                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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   160   6
  XQ LOSS WILD-TYPE 729  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    160    6
  XQ LOSS WILD-TYPE  729   16
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0             160               729
  1               6                16
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   186   3
  XQ LOSS WILD-TYPE 881   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    186    3
  XQ LOSS WILD-TYPE  881    9
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE             186               881
  MALE                 3                 9
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    83  93
  XQ LOSS WILD-TYPE 354 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     83   93
  XQ LOSS WILD-TYPE  354  454
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               83               354
  YES              93               454
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ LOSS MUTATED                            0                           148
  XQ LOSS WILD-TYPE                          1                           620
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ LOSS MUTATED                               23                   0
  XQ LOSS WILD-TYPE                            178                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ LOSS MUTATED                       1                                8
  XQ LOSS WILD-TYPE                     8                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER, SPECIFY
  XQ LOSS MUTATED                    3              6
  XQ LOSS WILD-TYPE                 14             40
D82V9, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                148               620
  INFILTRATING LOBULAR CARCINOMA                23               178
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                22
  MUCINOUS CARCINOMA                             3                14
  OTHER, SPECIFY                                 6                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"
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   120
  XQ LOSS WILD-TYPE                       144   624
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               144
  WHITE                                        120               624
[1] 4 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     7 155
  XQ LOSS WILD-TYPE  32 719
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      7  155
  XQ LOSS WILD-TYPE   32  719
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             155               719
[1] 2 2
[1] FALSE
